Prepared in cooperation with the Missouri River Recovery Program 

Development of Conceptual Ecological Models Linking 

Management of the Missouri River to Pallid Sturgeon 

Population Dynamics 

Open-File Report 2015-1038
 

U.S. Department of the Interior 

U.S. Geological Survey 
Cover photograph index: 

Background image: shaded relief map of the Missouri River drainage basin, US Geological Survey, EROS 

Data Center. 

Photographs by U.S. Geological Survey personnel 

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Prepared in cooperation with the Missouri River Recovery Program 

Development of Conceptual Ecological Models Linking 

Management of the Missouri River to Pallid Sturgeon 

Population Dynamics 

By Robert B. Jacobson, Michael J. Parsley, Mandy L. Annis, Michael E. Colvin, Timothy L. Welker, and Daniel A. James 

Open File Report 2015–1038

U.S. Department of the Interior 

U.S. Geological Survey 

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U.S. Department of the Interior 

SALLY JEWELL, Secretary 

U.S. Geological Survey 

Suzette M. Kimball, Acting Director 

U.S. Geological Survey, Reston, Virginia 2015

For product and ordering information:
 

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its natural and living resources, natural hazards, and the environment:
 

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Suggested citation: 

Jacobson, R.B., Parsley, M.J., Annis, M.L., Colvin, M.E., Welker, T.L., and James, D.A., 2014, Development of conceptual 

ecological models linking management of the Missouri River to pallid sturgeon population dynamics: U.S. Geological 

Survey Open-File Report 2015-1038, 47 p., http://dx.doi.org/10.3133/ofr20151038.

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Although this information product, for the most part, is in the public domain, it also may contain copyrighted materials as noted in the 

text. Permission to reproduce copyrighted items must be secured from the copyright owner. 

ISSN 2331-1258 (online) 

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Acknowledgments 

The authors would like to thank participants in the collaborative conceptual ecological modeling workshops held during August, 2013. 

We are also grateful for conscientious reviews of this report by Clayton Ridenour, U.S. Fish and Wildlife Service, Columbia, Missouri, 

George Jordan, U.S. Fish and Wildlife Service, Billings, Montana, and Steve Chipps, South Dakota State University, and by members 

of the Missouri River Independent Science Advisory Panel. 

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Contents 

Abstract ......................................................................................................................................................................... 1
 

Introduction.................................................................................................................................................................... 1
 

Background................................................................................................................................................................ 3
 

Conceptual Ecological Model Workshops .................................................................................................................. 4
 

Scope and Objectives ................................................................................................................................................ 7
 

Approach ..................................................................................................................................................................... 12
 

Component Model Structure .................................................................................................................................... 12
 

Population Augmentation Processes ....................................................................................................................... 14
 

Independent Drivers................................................................................................................................................. 14
 

Management and Restoration.................................................................................................................................. 14
 

Primary Ecological Factors....................................................................................................................................... 15
 

Secondary Ecological Factors.................................................................................................................................. 17
 

Primary Biotic Response.......................................................................................................................................... 18
 

Secondary Biotic Response ..................................................................................................................................... 18
 

Spatial Structure of the Conceptual Ecological Models............................................................................................ 19
 

Descriptions of Component Models ............................................................................................................................. 21
 

Upper River.............................................................................................................................................................. 21
 

Pre-spawn and Spawning Adults.......................................................................................................................... 21
 

Developing Embryos ............................................................................................................................................ 25
 

Free Embryos....................................................................................................................................................... 25
 

Exogenously-feeding Larvae ................................................................................................................................ 26
 

Juveniles .............................................................................................................................................................. 27
	

Lower River.............................................................................................................................................................. 28
 

Pre-spawn and Spawning Adults.......................................................................................................................... 28
 

Developing Embryos ............................................................................................................................................ 29
 

Free Embryos....................................................................................................................................................... 29
 

Exogenously-feeding Larvae ................................................................................................................................ 30
 

Juveniles .............................................................................................................................................................. 31
 

Summary and Conclusions......................................................................................................................................... 32
 

References Cited......................................................................................................................................................... 33
 

Appendix...................................................................................................................................................................... 38
 

Figures

Figure 1. Process steps envisioned for the Missouri River Pallid Sturgeon Effects Analysis. ...................................... 5
 

Figure 2. Population-level conceptual ecological model for pallid sturgeon................................................................... 8
 

Figure 3. Categories of conditions and processes ......................................................................................................... 9
 

Figure 4. Arrangement of conditions and process affecting transition between two life stages. .................................... 9
 

Figure 5. Hierarchical arrangement of essential ecosystem characteristics applied to spring-rise managed flows on 

the Missouri River. .................................................................................................................................................. 10
 

Figure 6. Pre-development and post-development range of pallid sturgeon in the Missouri and Mississippi river
 

basins ..................................................................................................................................................................... 11
 

Figure 7. Example of a component conceptual ecological model for pallid sturgeon effects analysis.......................... 16
 

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Tables 

Table 1. Descriptions of importance and uncertainty categories for CEMs.................................................................. 13
 

Table 2. Candidate working set of biologically dominant hypotheses. ......................................................................... 22
 

Conversion Factors 

International System of Units to Inch/Pound 

Multiply By To obtain 

Length 

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi) 

Area 

square meter (m2) 0.0002471 acre 

hectare (ha) 2.471 acre 

hectare (ha) 0.003861 square mile (mi2) 

Flow rate 

meter per second (m/s) 3.281 foot per second (ft/s) 

Inch/Pound to International System of Units 

Multiply By To obtain 

Density 

acres per mile 0.2515 hectares per kilometer 

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:
­

°F=(1.8×°C)+32
­

Temperature in degrees Fahrenheit (°F) may be converted to degrees Celsius (°C) as follows:
­

°C=(°F-32)/1.8
­

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Development of Conceptual Ecological Models Linking 

Management of the Missouri River to Pallid Sturgeon 

Population Dynamics 

By Robert B. Jacobson,

1 Michael J. Parsley,2 Mandy L. Annis,1 Michael E. Colvin,3 Timothy L. Welker,4 and 

Daniel James5 

Abstract 

This report documents the process of developing and refining conceptual ecological models 

(CEMs) for linking river management to pallid sturgeon (Scaphirhynchus albus) population dynamics 

in the Missouri River. The refined CEMs are being used in the Missouri River Pallid Sturgeon Effects 

Analysis to organize, document, and formalize an understanding of pallid sturgeon population 

responses to past and future management alternatives. The general form of the CEMs, represented by a 

population-level model and component life-stage models, was determined in workshops held in the 

summer of 2013. Subsequently, the Missouri River Pallid Sturgeon Effects Analysis team designed a 

general hierarchical structure for the component models, refined the graphical structure, and 

reconciled variation among the components and between models developed for the upper river (Upper 

Missouri & Yellowstone Rivers) and the lower river (Missouri River downstream from Gavins Point 

Dam). Importance scores attributed to the relations between primary biotic characteristics and survival 

were used to define a candidate set of working dominant hypotheses about pallid sturgeon population 

dynamics. These CEMs are intended to guide research and adaptive-management actions to benefit 

pallid sturgeon populations in the Missouri River. 

Introduction 

Conceptual models are used for a variety of purposes in resource management applications. A 

conceptual model is simply an abstract mental or graphical image of important parts of a system and 

how they are related. In an ecosystem context, conceptual models are defined as “graphic

representations of interactions among key ecosystems components, processes, and drivers” (Woodward 

and others, 2008, p. 60). Conceptual models may vary broadly in their structure and complexity 

(Gentile and others, 2001); those created for ecological applications can get very complicated and often 

evolve into complex process-based (Walters and others, 2000) or probabilistic (Rieman and others, 

2001; Stewart-Koster and others, 2010) computational models. 

Conceptual models are frequently cited as a necessary step in formal adaptive management in 

which stakeholders and scientists jointly develop a shared understanding of what affects an ecosystem 

or population, and then apply the model to predictions of biological responses (hypotheses) 

1 U.S. Geological Survey 2 U.S. Geological Survey 

3 Oregon State University 4 U.S. Army Corps of Engineers 5 U.S. Fish and Wildlife Service 

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under management scenarios (Walters, 1986). The conceptual model also functions as a teaching and 

communication tool in the adaptive management process. 

The purposes of the conceptual ecological models (CEMs) are presented in this report: 

•	 to provide a broad perspective on factors potentially affecting the endangered pallid 

sturgeon (Scaphirhynchus albus) populations in the Missouri River; 

•	 to serve as a communication tool about those factors and their possible linkages to 

management and restoration actions; 

•	 to provide a structure from which priority hypotheses will be selected based on their 

importance in explaining pallid sturgeon population dynamics and their value in guiding 

Missouri River management decisions. 

Priority hypotheses developed from the CEM components presented in this report will be used 

in a formalized effects analysis (Murphy and Weiland, 2011) to guide structured decision making in 

the Missouri River Recovery Program (MRRP). The Missouri River Pallid Sturgeon Effects Analysis 

(EA) is charged with a multistep process, resulting in four reports during phase 1 (fig. 1): 

•	 develop CEMs to document and illustrate driver-stressor-response ecological 

relationships. The CEM development process is documented in the present report. 

•	 develop a hierarchy of hypotheses to depict relations in the CEMs. The process of 

hypothesis formulation and filtering will be documented in the second report in the 

series and as a US Geological Survey Open-File Report 

•	 compile and assess available information and modeling resources that can be used to 

understand historical and future changes of pallid sturgeon populations. This will be 

the third report in the series. 

•	 compile an integrative, lines-of-evidence approach using best available science to assess 

hypotheses emanating from the hypothesis development process. This will include the 

best available combinations of qualitative and quantitative models, theoretical and 

empirical data, and expert opinion. This synthesis will be documented in an initial EA 

integrative report, that will be published as a U.S. Geological Survey Scientific 

Investigations Report. 

These documents from the EA are intended to inform MRRP decisions about how to best 

manage the Missouri River and its resources to meet species objectives and authorized purposes. 

For pallid sturgeon in the Missouri River, the species objective is to “avoid jeopardizing the 

continued existence of the pallid sturgeon from US Army Corps of Engineers actions on the 

Missouri River.” (U.S. Fish and Wildlife Service, unpub. data, 2013). The U.S. Fish and Wildlife 

Service (USFWS) notes that this objective is consistent with species recovery goals (U.S. Fish and 

Wildlife Service, 2014) but is specific to Missouri River management actions. 

The CEM and quantitative model framework developed through the EA are intended to form 

part of the framework for future adaptive management in the Missouri River. Although drafting of the 

adaptive management plan is not currently (2014) complete, we anticipate that the plan will include an 

ongoing assessment process similar to the EA, whereby new learning from monitoring, assessment, 

and research efforts will be used to improve management actions with time. An important part of this 

effort will be the option to refer to the CEMs documented in this report if the need arises to provide 

new hypotheses to explain observed changes in pallid sturgeon populations. 

The objective in developing the CEM is to provide a “global” set of process relations that may 

affect pallid sturgeon population dynamics. These hypotheses were developed through the expert 

opinion of sturgeon biologists and river scientists. The global set is a beginning point from which 

hypotheses can be progressively prioritized for quantitative simulation modeling based on their 

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relevance in explaining pallid sturgeon population dynamics and their value in guiding decision 

making. These models will seek to predict survival probabilities at critical life stages as a function of 

management or restoration actions. The framework has been developed so the component models can 

be linked through a population model to provide a framework for assessing effects of management 

actions at the population level. 

Background 

The pallid sturgeon is an endangered, benthic fish endemic to the turbid Missouri and 

Mississippi Rivers and the lower parts of larger tributaries. The species was listed as endangered 

under the Endangered Species Act in 1990 (Federal Register, 1990) and in 2000 the USFWS 

published a biological opinion that indicated that U.S. Army Corps of Engineers (USACE) operations 

of the Missouri River were likely to jeopardize its existence. The primary stressors responsible were 

habitat alteration related to changes in flow regime and channel form among a long list of potential 

threats (Dryer and Sandvol, 1993). The biological opinion and a 2003 amendment defined elements 

of a reasonable and prudent alternative (RPA) to avoid jeopardy to these Missouri River populations 

(U.S. Fish and Wildlife Service, 2000, 2003). The pallid sturgeon RPA elements include (among 

others) implementation of adaptive management, monitoring, and research, restoration of 20-30 acres 

per mile (5-7 ha/km) of shallow-water habitat (SWH), increased pallid sturgeon propagation and 

augmentation, and flow enhancements from Fort Peck and Gavins Point dams. 

Large-scale restoration of Missouri River channel and floodplain habitats date from the 

Missouri River Bank Stabilization and Navigation Project Fish and Wildlife Mitigation Program 

(Mitigation Program), which was authorized in the Water Resources Development Act of 1986, 5 

years after completion of the Bank Stabilization and Navigation Program (BSNP) (National Research 

Council, 2002). The Mitigation Program was intended originally to mitigate for habitat losses due to 

the BSNP, with a goal of restoring 166,750 acres of channel, sandbar, and meander belt habitat, 

approximately 32 percent of the estimated lost habitat (U. S. Army Corps of Engineers, 1981). The 

goals for compliance with the amended biological opinion and for the Mitigation Program were 

formally incorporated into the MRRP in the Water Resources Development Act of 2007 (WRDA 

2007). The WRDA 2007 also authorized mitigation projects along the main stem Missouri River in 

the upstream segments of the river, including Montana, North Dakota, Nebraska, and South Dakota, as 

well as restoration projects in the Yellowstone River and its tributaries in Montana and South Dakota. 

The WRDA 2007 additionally authorized use of USACE funding to assist the Bureau of Reclamation 

with planning and construction of fish passage and entrainment protection at the Lower Yellowstone 

Project’s Intake Diversion Dam (Intake Dam) and associated irrigation canal headworks. 

Implementation of fish, wildlife, and habitat restoration activities on the Missouri River has 

been guided by principles of adaptive management since adoption of the 2000 "Missouri River 

Biological Opinion" (U.S. Fish and Wildlife Service, 2000) and the 2001 "Missouri River Mainstem 

System Master Water Control Manual" (U.S. Army Corps of Engineers, 2001). Adaptive management 

was adopted more formally with creation of the Missouri River Recovery Implementation Committee 

(MRRIC), an advisory group to the USACE authorized in the WRDA 2007, and committees or 

affiliates of MRRIC that are closely aligned with adaptive management: the Science and Adaptive 

Management (SAM) work group and the Independent Science Advisory Panel (ISAP). Emphasis on 

construction of CEMs and implementation of effects analyses were prominent recommendations of the 

ISAP to promote robust adaptive management of the Missouri River and its imperiled species (Doyle 

and others, 2011). 

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Two levels of a conceptual model are presented here to apply to an understanding of ecological 

effects on pallid sturgeon populations. The population-level conceptual model is based on models 

documented in Wildhaber and others (2007, 2011). This model shows key components of a 

population model in which conditions and processes contribute to transition probability from one life 

stage to the next (fig. 2). In addition to identifying key life stages and life-stage transitions (survival 

probabilities), this population-level model shows the spatial dimension of habitat use by the pallid 

sturgeon. Because the pallid sturgeon can disperse or migrate for hundreds of kilometers in a season, 

different life stages play out in different parts of the river, generally with spawning habitat at the apex 

of upstream reproductive migrations and rearing habitat for larval and juvenile fish thought to occur 

substantially farther downstream as young fish disperse (Braaten and others, 2008; Braaten and others, 

2012; DeLonay and others, in press). 

The second level of CEM (the component model) addresses the conditions and processes 

affecting survival probabilities for each life stage. The component level was described in Wildhaber 

and others (2007, 2011) as linkages among processes. Processes included human-related direct 

mortality, non-human direct mortality (predation), rate-affecting factors (such as disease, habitat, prey 

availability, competition, and contaminants), and abiotic and biotic condition factors such as flow 

regime, sediment regime, temperature, and non-native and native fishes (fig. 3). Combinations of 

processes and conditions thought to be most important were shown as interactions that affected 

survival probabilities for each life-stage transition (fig. 4). 

Another CEM for pallid sturgeon was developed for application to Missouri River restoration 

activities with emphasis on hierarchical propagation of management actions through essential 

ecosystem characteristics (EECs) of abiotic effects, habitat effects, and biotic responses (Jacobson and 

Berkley, 2011). Jacobson and Berkley (2011) showed a specific application to assessment of how 

flow modifications may affect pallid sturgeon reproductive ecology (fig. 5). Jacobson and Berkley 

(2011) also demonstrated how the hierarchical approach could be useful in understanding causal 

linkages and applied to allocation of monitoring and assessment resources. A similar hierarchical 

approach to conceptual ecological modeling was suggested by the Missouri River ISAP for application 

in understanding species recovery (Doyle and others, 2011). 

Conceptual Ecological Model Workshops 

The conceptual models discussed in this report arose from a series of workshops hosted by the 

USACE and USFWS in 2013 under the auspices of the USACE Missouri River Recovery Program 

(MRRP). Workshop participants were sturgeon biologists, landscape ecologists, and river experts 

from State and Federal agencies. Workshop goals were to review and refine CEMs and to develop 

objectives to be used during the planning and adaptive management process for the pallid sturgeon. 

Because of substantive difference in management issues, separate workshops were convened for the 

lower river and the upper river (fig. 6). The lower river group met July 17 and 18 and the upper river 

group met July 23 and 24. 

During the lower river workshop, the attendees adopted a graphical format in which 

hierarchical component-level models feed into individual life-stage survival probabilities. This 

general structure was thought to lead effectively into a stage-based population model and was 

therefore adopted as the eventual end point of the conceptual modeling process. These ideas were 

subsequently accepted by the upper river workshop attendees. 

4 
Figure 1. Process steps envisioned for the Missouri River Pallid Sturgeon Effects Analysis. A, Broad-scale view of 

the EA role in the ongoing process of assimilation and evaluation of information developed through adaptive 

management of the Missouri River. B, Detail of steps in phase 1 of the EA. The present report is the CEM 

Development Report. Subsequent steps assess available science information, document hypothesis filtering, and 

synthesize a lines-of-evidence approach to evaluating management effects in pallid sturgeon populations. 

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The original guidance for the workshops included geographic scope and some working 

assumptions. As the workshops progressed, some of these assumptions were relaxed or revised, as 

indicated by determinations listed below: 

•	 Guidance.- The geographic scope is the Missouri River from Fort Peck downstream to 

the confluence of the Mississippi River and includes specific elements of the Biological 

Opinion as amended, like the Intake Diversion Dam Project on the Yellowstone River. 

o	 Determination.- During the workshops, it was determined that the reservoir and 

inter-reservoir reaches from the headwaters of Lake Sakakawea (not shown) to 

Gavins Point Dam would not be considered explicitly in this phase of conceptual 

ecological modeling. The potential for inter-reservoir reaches with clear, cold 

water and hydropeaking releases to contribute to pallid sturgeon recovery was 

considered low but may be usefully considered in a subsequent phase of analysis 

o	 Determination.- It was also determined that processes and conditions acting in 

Missouri River tributaries and the Mississippi River should be included in the CEMs 

if those processes and conditions would affect population processes in the target 

geographic area. 

•	 Guidance.- Conceptual ecological model and objectives are focused on
	

MRRP responsibility to avoid jeopardy to listed species.
	

o	 Determination.- During the workshops, it was determined that the CEMs should be 

more broadly constructed so as to consider a wide range of conditions and processes 

beyond those that are the responsibility of the MRRP. This decision was based on 

the understanding that the CEMs should be illustrative of the universe of hypotheses 

determining pallid sturgeon population dynamics to provide explanation for 

instances in which MRRP actions to avoid jeopardy are unsuccessful because of 

conditions and processes outside of MRRP control. 

•	 Guidance.- The drivers identified in the species CEMs will be limited to the
	

USACE management actions that have an effect on species performance.
	

o	 Determination.- Similar to the logic articulated in the previous bullet, the 

workshop participants believed that the CEMs should be more broadly constructed 

so as to consider all conditions and processes, even those that are not the 

responsibility of the MRRP. It is anticipated that during subsequent steps in the 

effects analysis process, priority hypotheses will be identified based on their 

relevance to pallid sturgeon population dynamics and their importance to decision 

making under the MRRP. 

•	 Guidance.- The RPA elements included in the CEMs will be limited to those included 

within the 2003 "Missouri River Biological Opinion" (U.S. Fish and Wildlife Service, 2003). 

Our aim is not to develop models that include “everything” that may affect the species. 

Rather, the models should be focused on those issues relevant to decision making for the 

MRRP. The models developed in these workshops are intended to illustrate the effects of 

USACE operations and restoration actions on the listed species; therefore, the models should 

have a bias toward management actions and how they propagate through the ecosystem. 

o	 Determination.- The workshop participants believed that some relevant management 

actions may not have been envisioned when the 2003 "Missouri River Biological 

Opinion" (U.S. Fish and Wildlife Service, 2003) was drafted, and the CEM process 

was a useful venue for developing and evaluating new potential actions that might be 

feasible under various existing authorities. 

At the end of the workshops, smaller teams were assigned to clarify the graphic models and 

to populate spreadsheets that were designed to describe every box and arrow in the graphic models; 6 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

this phase of model revision was completed by September 15, 2013. The draft models were provided 

to interested stakeholders and members of the public for technical review during a 30-day review 

period ending on October 30, 2013. The review comments were compiled by the MRRP, and the 

comments, model materials, and workshop notes were supplied to the members of the Missouri 

River Pallid Sturgeon EA team (the authors of this report) in preparation for the next 

phase of refinement. 

Purpose and Scope 

This report is the first in a series intended to document the Missouri River Pallid Sturgeon EA 

process (fig. 1). In this report, we present and describe refined global, component CEMs for pallid 

sturgeon in the Missouri River. The models are described as “global” to denote that they include a 

large number of potential relations among conditions and processes, each of which can be considered a 

hypothesis or part of a hypothesis. It is acknowledged that some relations may be highly uncertain, 

some may be considered to have small probability of increasing survival and population growth, and 

some may be tenuously linked to management actions under the MRRP. Nevertheless, the universe of 

potential processes is considered important to encourage critical thinking about pallid sturgeon 

population dynamics and to set the stage for subsequent refinement and prioritization of hypotheses for 

simulation modeling. 

The individual life-stage models are described as “component” to denote that they apply to 

conditions and processes that determine discrete life-stage survival probabilities. The component 

models are linked conceptually and computationally through the stage-based population-level model 

(fig. 2), which, if properly structured and parameterized, will be useful in simulating population 

dynamics responses to management actions. The EA team has determined that hypotheses that address 

population augmentation (stocking) fit best within the population-level model. 

This report documents the approach used to refine the component conceptual models resulting 

from the workshops and provides a narrative describing key relations among ongoing, proposed, and 

potential future management actions and ecological factors that alter survival probabilities. The 

objective of this report is to present component CEMs that clearly, logically, and systematically 

illustrate the current understanding of the universe of conditions and processes that may affect pallid 

sturgeon population dynamics in the Missouri River. Although we have revised the models that came 

out of the workshops in an attempt to achieve a uniform format, we have maintained as much of the 

structure and priorities of the original workshop products as possible. The intent is for these models 

to act as a robust foundation for subsequent prioritization of hypotheses and construction of simulation 

models; however, it is also expected that the models will be revised continually as learning is updated 

through an adaptive management process that includes robust research, monitoring, assessment, and 

learning (fig. 1). 

The CEMs are considered the first step in a process to prioritize and focus on essential models 

needed to inform management decisions faced by the MRRP. The fundamental objective is to inform 

decisions that will avoid and prevent jeopardy for the pallid sturgeon in the Missouri River (unpub. 

data, 2013). Eventually, CEM graphics and descriptions will be refined into a set of working 

dominant hypotheses that represent a scientific perspective on factors that plausibly contribute to 

population decline of the pallid sturgeon in the Missouri River. These hypotheses may be similar to 

threats listed under the pallid sturgeon recovery plan (U.S. Fish and Wildlife Service, 2014) but will 

be more geographically focused on the Missouri River. A subsequent step will develop hypotheses 

for the multiple pathways from management actions that may lead to increase in survival or decrease 

in mortality at each life stage; these will be referred to as working management hypotheses. 

7 
Figure 2. Population-level conceptual ecological model for pallid sturgeon. From Wildhaber and others (2007, 2011). 

8
	
Figure 3. Categories of conditions and processes (Wildhaber and others, 2011). 

Figure 4. Arrangement of conditions and process affecting transition between two life stages (Wildhaber and others, 2011). 

9
	
Figure 5. Hierarchical arrangement of essential ecosystem characteristics applied to spring -rise managed flows on the 

Missouri River (Jacobson and Berkley, 2011). 

10 
Figure 6. Pre-development and post-development range of pallid sturgeon in the Missouri and Mississippi river basins (DeLonay and others, in press). 

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Management hypotheses will consider actions that could logically be accomplished to aid species 

recovery without testing for whether they fall within USACE authorities. The management hypotheses 

will also be more spatially explicit because some management options will be more effective in certain 

areas. Management hypotheses will also have similarities to recovery tasks in the pallid sturgeon 

recovery plan (U.S. Fish and Wildlife Service, 2014) but will address the fundamental objective of 

removing and precluding jeopardy, rather than specifically recovering the species. 

The final step in the prioritization process will involve filtering the management hypotheses 

for those that fall within USACE authorities and jurisdictions. This set of initially modeled 

hypotheses will guide near-term modeling by the EA team to apply to management decisions. 

Identification of the bounds of actionable hypotheses will be the joint responsibility of USACE and 

USFWS. 

Approach 

The component CEMs are designed in a hierarchical, left-to-right structure, culminating in a 

survival probability. The survival probabilities correspond to the survival probabilities in the 

population-level model (fig. 2), such that processes and conditions in the component models are 

linked to survival from one life stage to the next. In this manner, the effects of specific management 

actions can be propagated through the component models to alter survival probabilities, with 

consequent effects on population dynamics. The overall structure is that of a stage-based populationlevel model and corresponds to the general concept of application of population viability analysis in 

effects analysis discussed by Murphy and Weiland (2011). Published work on pallid sturgeon 

populations and models provides understanding of population dynamics under current (2014) 

conditions (Bajer and Wildhaber, 2007; Steffensen and others, 2013a, 2013b), and an initial structure 

for incorporation of future management and ecological effects. 

Separation of management actions, conditions, and processes by life stage is critical for the 

pallid sturgeon because historical alterations, engineering features, and life-stage processes vary 

spatially and temporally within the sturgeon’s home range (the total length of river used by the pallid 

sturgeon during its life). Because survival probabilities vary considerably by life stage, the differential 

survival probabilities may be important in prioritizing management actions. Indeed, workshop 

participants determined that present knowledge of survival probabilities indicates that only five of 

eight life-stage transitions shown in figure 2 were relevant to understanding present-day population 

dynamics and would be considered in the component CEMs. The assumed value of a stage-based 

model (compared to an age-based model) is that transitions from one stage to another are thought to 

be biologically important and likely associated with abruptly increased or decreased chances of 

mortality. Developmental stages can be problematic to define, however, especially if transitions 

between them are not abrupt, such as the transition from exogenously feeding larvae to juveniles. 

Moreover, developmental stages do not have a 1:1 relation with ages or with sampling gears, 

especially at early life stages. Therefore, although the stages selected for these CEMs may provide 

biological insights, they may need to be modified in the future to conform to fish sampling datasets or 

modeling needs, or they may need to be supplemented to accommodate new insights into pallid 

sturgeon biology. 

Component Model Structure 

The component models are arranged hierarchically in a modification of a driver-stressor format 

(fig.7). In recognition that the ultimate drivers of river-system change are anthropogenic or 

geologic/climatic, only factors in the far left column are considered to be independent drivers. Each 

pair of columns, from left to right, can be considered a driver-stressor pair, with the final column being 

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the ultimate biotic response (secondary biotic response, or change in survival probability). The 

columns categorize the hierarchy of factors into management and restoration, primary ecological 

factors, secondary ecological factors, and primary biotic responses. The columns are similar to tiers 

of EECs developed to provide hierarchical organization in other CEMs (Harwell and others, 1999; 

Lubinski and Barko, 2003; Jacobson and Berkley, 2011). An important feature of the columns (and 

tiers of EECs) is that uncertainty in predictions and biological relevance generally increases to the 

right, moving from abiotic time series to habitat (availability of biological important physical spaces 

in time and space) to biotic responses (growth, reproduction, survival). A critical question faced by 

many adaptive management programs is how to allocate resources to predictive modeling, 

monitoring, and assessment among the columns to provide the most cost effective information for 

decision making (Jacobson and Berkley, 2011). 

The refined CEM diagrams include nested boxes allowing for additional levels of hierarchical 

organization within each column. The bounding boxes are broad descriptions of ecosystem factors and 

are common to all component models. The colored boxes within the bounding boxes are more specific 

factors; these factors vary by component model to emphasize that different factors are thought to be 

important in different locations and at different life stages. The nested structure provides additional 

flexibility for depicting relations among factors because the linking arrows can be attached to either the 

bounding boxes or to the specific boxes depending on how modeling needs and (or) available 

information dictate that the relations should be lumped or split. 

Arrows indicate linkages among factors and are depicted by nine different combinations of 

colors and patterns based on workshop participants’ understanding of relative uncertainty and 

importance to population dynamics. Although many more potential linkages could have been 

constructed, the linkages shown in the diagrams present those which workshop participants considered 

to have at least a small, modifying effect. Assignments to uncertainty and importance categories 

occurred during the modeling workshop and have been maintained with few revisions for the versions 

presented here. Relative importance is symbolized as a progression from dotted to dashed to solid 

lines, reflecting low to high importance. Relative uncertainty is symbolized as a progression from 

black to red, reflecting low to high uncertainty. A qualitative description of the categories is shown in 

table 1. Assignment to uncertainty and importance categories is expected to change as the models go 

through subsequent phases of review and revision, and as additional information becomes available. 

Table 1. Descriptions of importance and uncertainty categories for conceptual ecological models. 

Type Label Description 

Importance 

Uncertainty 

High 

Moderate 

Low 

High 

Moderate 

A link that is known or thought to have a direct and substantive 

effect in altering another condition or process. 

A link that is known or thought to have an indirect, modifying effect 

another condition or process. 

A link that is known or thought to have a small modifying effect on 

another condition or process. 

A link with no published literature to support understanding. 

A link with some support from published studies on other species or 

rivers. 

Low A link supported by information from peer-reviewed studies specific 

to the question and species. 

13 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Population Augmentation Processes 

An additional CEM component is designed specifically to describe population augmentation 

through propagation. As represented in the population model (fig. 2), propagation occurs as temporary 

or permanent removal of broodstock from the adult population and as stocking of hatchery-reared fish 

in exogenously feeding larvae and juvenile stages (mostly as juveniles). The conditions and processes 

that influence how propagation takes place are information based rather than ecological. That is, 

propagation management decisions are made based on information on relative survival of different age 

classes, relative survival in different parts of the river, and parental genetics as they relate to 

understanding of the natural, underlying genetic composition of the population. These decisions are 

represented on the diagram for the population-level model (fig. 2). 

It is possible that wild-produced and hatchery-produced fish will respond in different ways to 

the same environmental factors, resulting in differential survival probabilities. Hatchery fish may be 

poorly acclimated to natural conditions, may have difficulty adapting to natural food sources, may lack 

imprinting to water quality and habitat conditions, or may harbor disease in greater proportion than the 

natural environment. Therefore, the population-level conceptual model provides capability for 

tracking hatchery fish separately from wild-produced fish, which is illustrated in the population-level 

model (fig. 2) by the dual-color of the boxes representing numbers of wild and hatchery individuals in 

each life stage. Although hatchery and wild-produced fish are not depicted in the presentation of the 

component models, implementation of dual tracking in the population model may also require 

duplicate component models to capture the differential survival between them. 

Independent Drivers 

Independent drivers are categorized into (1) social, political, and economic drivers of change; and (2) 

physical factors (climate, geology, land use, and non-USACE management and engineering) that 

control fluxes of water, energy, sediment, and chemical constituents into the system or present hard 

geologic or engineered constraints to river processes. The two categories are related, but the relation is 

asymmetric. Physical factors clearly influence social, political, and economic drivers of change by 

determining biophysical capacity of the Missouri River, or, for example, imposing extreme events 

such as floods and droughts. Because of the complexity of decision making at the scale of the 

Missouri River, the linkage is symbolized as highly important but uncertain. Social, political, and 

economic drivers of change affect physical factors mainly through land-use change and non-USACE 

management activities. Examples might be basin-scale changes in agricultural production as a result 

of biofuels technology or international demand for commodities, or construction of reservoirs or 

channel stabilization projects outside of USACE MRRP authorities. These factors are symbolized as 

moderate importance and highly uncertain to reflect the judgment that social, political, and economic 

actions sufficient to change physical factors in the Missouri River basin are likely to be small relative 

to the effects of the existing main stem reservoirs and channel engineering. Moreover, the effects of 

these drivers are uncertain because of difficulties predicting the net effects of decentralized actions in 

the basin. The independent drivers are identical for all 10 component models although the nature of 

their linkages to other factors varies geographically. 

Management and Restoration 

There are many linkages from independent drivers to the column of factors labeled 

"Management and Restoration" in figure 7. For the purposes of these CEMs, management and 

restoration actions relate specifically to the USACE management actions, with the actions of other 

agencies represented as drivers. This structure follows the substantive effect that USACE 

management and restoration actions have on the main stem Missouri River and from the intent to 14 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

apply these models in the near term to MRRP decision making. The management and restoration 

factors modify inputs from the physical and the social, political, and economic drivers. This 

conceptualization of how management and restoration actions work in the Missouri River system 

emphasizes their limits. A specific example is the limit of the reservoir system to filter basin-wide 

floods and droughts; the reservoir system acts as a filter that modifies magnitude, frequency, duration, 

timing, and rate of change but is not adequate to completely counteract climatic extremes imposed on 

it (Jacobson and Berkley, 2011). Some linkages bypass the management and restoration column, 

indicating those management decisions or conditions propagate to the river but are not affected, or are 

minimally affected, by USACE projects. An example would be potential water contamination by 

urban wastewater discharges or agricultural runoff. 

Management and restoration factors have been subdivided into two bounding boxes indicating 

the two broad categories of management actions under USACE authorities. The first collects factors 

related to channel management and restoration, including channel configurations (channelization and 

channel-training structures) and bank stabilization. Channel reconfigurations include changes to 

channel geometry to result in increased complexity and habitat provision while maintaining an 

acceptable level of authorized purposes. Bank stabilization was given a separate category because 

some stabilization activities in the Upper and Lower Missouri Rivers are independent of the BSNP. 

The second bounding box includes factors related to the main stem reservoir system, including 

operating rules, fish-passage structures, water-quality structures, and locations. The factors represent 

possible actions that might be applied to operations of the main stem reservoir system even if 

present-day engineering does not accommodate them. For example, fish-passage and water-quality 

structures (structures or processes to vary temperature, dissolved oxygen, and (or) sediment 

concentrations in releases) were never designed for the main stem dams but could possibly be 

installed. The category of passage structures includes potential fish-passage designs for the Intake 

Dam on the Lower Yellowstone River. Locations refer to present or future locations of dams on the 

main stem system. The locations category has specific application to consideration of how dam 

locations operate to impede migrations, dispersal, and survival of pallid sturgeon, and how those 

locations interact with the natural genetic structure of the pallid sturgeon metapopulation. 

The management and restoration factors are identical for all 10 component models although the 

importance and uncertainty of linkages vary considerably. A large difference among component 

models is the high importance and certainty ascribed to channel configuration and bank stabilization on 

the Lower Missouri River, and the relative low importance of channel engineering on the Upper 

Missouri River. Another substantive difference is the relatively long section of channel in the lower 

river that integrates large variation in climate, geology, and land use from large tributaries to affect 

sediment regime, water-quality regime, and flow regime. The Lower Missouri River also allows for 

extremely long, potential migration and drift distances, as much as 2,000 miles, by connection with the 

Mississippi River. In contrast, the upper river is fragmented into a 220-mile segment of the Upper 

Missouri River and a 234-mile segment of the Yellowstone River. 

Primary Ecological Factors 

Primary ecological factors are abiotic physical and chemical characteristics of the river 

ecosystem. Three of them are described as regimes (that is, time series of fluxes or concentrations 

that can be described in terms of magnitude, frequency, duration, timing, and rate of change). The 

flow regime frequently receives the most interest in river management and restoration because it 

has been described as the master variable for aquatic riverine ecosystems under the assumption that 

15 
 Figure 7. Example of a component conceptual ecological model for pallid sturgeon effects analysis. 

16
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

other characteristics of aquatic ecosystems, including sediment regime, water-quality regime, and 

channel morphology, adjust in response (Poff and others, 1997). In highly engineered river systems, 

however, the flow regime is typically decoupled from sediment, water quality, and channel 

morphology (Jacobson and Galat, 2006, 2008; Poff and others, 2009) because dams interrupt sediment 

fluxes and alter water-quality characteristics like transport of organic material, nutrients, dissolved 

oxygen, and temperature. In minimally altered rivers, channel morphology and associated physical 

habitats are expected to adjust to flow and sediment regimes imposed on them, with flow regime 

being the dominant control; however, in engineered rivers like the Lower Missouri River, the channel 

morphology is controlled mostly by river-training structures. 

All 10 component models have a bounding box under primary ecological factors titled “Flow, 

geomorphology, hydraulics, and water-quality interactions.” The complex linkages depicted among 

the specific factors (channel morphology, sediment regime, water-quality regime, and flow regime) 

illustrate the mutual adjustments and feedbacks that are known to exist in dynamic river channels. In 

more natural channels (for example, the Upper Missouri and Yellowstone Rivers) the adjustment might 

be lumped as the bounding box and could be considered to be dominated by flow regime; however, 

because channelization has been a major stressor to the Lower Missouri River and because channel 

reconfiguration has been a dominant management strategy (and RPA under the 2003 Biological 

Opinion), we separate the specific factors of the adjustment process. The adjustments are particularly 

important because they introduce uncertainty in predictions of the equilibrium end state of physical and 

water-quality habitat and when adjustment will be achieved. The complex configuration was retained 

for the upper river CEMs to address the potential effects of bank stabilization or possibly channel 

reconfiguration for habitat improvements. Because there is less direct engineering of the channel and 

banks in the upper river, the adjustments are likely less important in determining physical and chemical 

habitat. 

Longitudinal connectivity is a primary ecological factor that operates at a broader scale and is 

therefore not shown as interacting within the bounding box. Longitudinal connectivity refers to the 

fragmentation of the main stem Missouri and Yellowstone Rivers by dams or reservoirs, a factor that 

has substantial importance in the pallid sturgeon life cycle because reproductive sturgeon have been 

documented migrating hundreds of kilometers upstream and larvae have the potential to drift and 

disperse hundreds to more than 1,000 kilometers downstream (Kynard and others, 2002; Braaten and 

others, 2008; DeLonay and others, 2009; Braaten and others, 2012; DeLonay and others, in press). 

Lack of longitudinal connectivity in the main stem and in some tributaries has limited upstream 

migration and downstream dispersal. 

Secondary Ecological Factors 

Secondary ecological factors are categorizations of conditions that result from primary 

ecological factors; categorizations are classified into bounding boxes of physical habitat, water quality 

(chemical habitat), and aquatic community composition (biotic habitat). Physical habitat, chemical 

habitat, and biotic habitat are each characterized in terms of dynamics (that is, described in terms of 

how habitat varies with time and through space according to concepts of analysis of hydrologic time 

series and patch dynamics; Pickett and White, 1985; Poff and others, 1997; The Nature Conservancy, 

2005; Jacobson, 2013). Variability in space and time arises from the complex interactions of channel 

morphology, flow regimes, water-quality regimes, sediment regimes, and life cycles of aquatic 

organisms that may act as food sources, predators, competitors, or disease vectors. 

The bounding boxes are common to all 10 component models but the specific factors and how 

they are linked vary by life stage and location. Within the physical habitat bounding box, hydraulics 

17 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

(spatial and temporal distributions of depth, velocity, and turbulence) and substrate characteristics are 

inter-related through the sediment transport capacity of the river, except in cases where substrate is 

associated with engineered structures (such as revetment rock) or bedrock exposures. Stability, 

quality, and quantity are particularly important aspects of substrate characteristics because of the 

benthic orientation of pallid sturgeon and, in particular, the role of substrate in spawning, fertilization, 

incubation, and hatching of adhesive eggs, and the production of forage for later life stages. 

The water-quality bounding box contains specific factors that vary by life stage and location. 

Although many water-quality parameters related to habitat suitability could be defined, we emphasize 

water temperature, dissolved oxygen, turbidity, and contaminants as four factors of potential 

importance. The category of contaminants is particularly broad and may include 

dichlorodiphenyltrichloroethane (DDT) and its metabolites, polychlorinated biphenyls (PCBs), 

chlordane, mercury, selenium, and cadmium or other metals (Ruelle and Kennlyne, 1993), or other 

endocrine disrupting chemicals (DeLonay and others, 2009). 

The aquatic community bounding box is also relatively broad in nature and varies considerably 

among component models. This bounding box includes elements of the aquatic community that 

contribute food to the pallid sturgeon or present sources of predation, competition, or disease (either as 

pathogens or as vectors for pathogens). For reproductive pallid sturgeon, the aquatic community 

includes the congeneric shovelnose sturgeon (Scaphirhynchus platorynchus), which has been thought 

to present a hybridization risk (Dryer and Sandvol, 1993; Schrey and others, 2011). Characteristics of 

the aquatic community are also linked in various ways to characteristics of physical and chemical 

habitat. The linkages within the "Secondary Ecological Factors" column provide potential for complex 

hypotheses to explain lack of recruitment in pallid sturgeon; for example, changes in physical habitat, 

although not affecting habitat use by pallid sturgeon directly, may have diminished habitat suitability 

for prey species, thereby diminishing food availability and consequent growth rates of juveniles and 

adults. 

Primary Biotic Response 

The "Primary Biotic Response" column is intended to describe specific biotic responses of 

pallid sturgeon to primary and secondary ecological factors. Primary biotic responses varied 

considerably among component models but were generally classified into three types: growth and 

condition, direct mortality, and reproductive behaviors. Growth and condition relate to factors that 

describe the bioenergetics of the fish (the integration of energy inputs and expenditures that 

determine somatic and gonadal growth). Lack of growth at a critical level may lead to starvation and 

mortality, or increase susceptibility to direct mortality. Direct mortality refers to sources of 

mortality not directly related to bioenergetics, including predation, removal (including harvest, 

entrainment, and impingement on screens, dredges, or props), toxins, and disease. Reproductive 

behaviors and synchrony are specific to spawning adults and include complex interactions between 

environmental variables and fish behavior that conceptually influence migration, aggregation, 

spawning site selection, and gamete placement during spawning and fertilization. 

Secondary Biotic Response 

All component models lead to one end point, the secondary biotic response or survival 

probability to the next life stage. Most, but not all, linkages from cause to effect propagate through 

each of the columns to the survival end point. Some linkages bypass parts of the structure. For 

example, removal of adult fish by harvest links directly to social, political, legal, and economic drivers 

of change (for example, through fish consumption advisories, poaching, and the worldwide market for 

caviar) instead of propagating through ecological factors. 

18 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

This structure – based on component models leading to survival probabilities for each life stage 

– is generally useful for a stage-based population-level model. One complication is dealing with transgenerational and trans-life stage effects. Such effects may not cause a decrease in survival for gametes 

or the next life stage but may instead manifest as lower survival probability during subsequent life 

stages. A trans-generational example is when lack of fitness in a reproductive adult results in delayed 

growth and lower fitness of embryos or larvae, resulting in increased mortality transitioning to later life 

stages. Trans-stage effects are situations where an individual survives a life stage but with reduced 

fitness so survival during later stages is diminished. Trans-generational or trans-life stage effects were 

not emphasized during the modeling workshops. If trans-generational or trans-life stage hypotheses 

emerge as priorities, they can be accommodated in the component models by defining another class of 

secondary biotic response that allows survival but results in enhanced mortality probability at later life 

stages. Trans-generational and trans-stage connections were added to the CEMs as a secondary 

ecological factor conditioning response and as secondary biotic responses transferring fitness or 

contaminant loads to the next life stage (fig. 7). 

Spatial Structure of the Conceptual Ecological Models 

Emerging data on population genetics support the notion that before development of the river, 

the metapopulation of pallid sturgeon was spatially structured, perhaps related to episodic genetic 

isolation during Pleistocene glacial advances and reorganization of the Missouri River drainage 

network (Campton and others, 2000; Tranah and others, 2004; Schrey and Heist, 2007; Schrey and 

others, 2011; DeLonay and others, in revision). One genetic group has been identified that is 

characteristic of the Upper Missouri River in Montana and North Dakota, another group is prominent 

in the Middle Mississippi and Atchafalaya Rivers, and a third genetically intermediate group is 

prominent in the Lower Missouri River, downstream from Gavins Point Dam (Schrey and Heist, 

2007). The Upper Missouri River group was most distinct, and less genetic differentiation was 

observed between the Lower Missouri River and the Middle Mississippi and Atchafalaya Rivers 

groups. 

Fragmentation of the Missouri River by dams exerts an additional, interacting spatial structure 

on the underlying, natural structure of the genetic subpopulations (fig. 6). There are no passage 

facilities at the main stem dams for volitional upstream passage. Only a few pallid sturgeon have 

been collected upstream from the Melvin Price Lock and Dam on the Mississippi River. Several 

shovelnose sturgeon have been documented passing over or around Intake Dam on the Yellowstone 

River (Tews, 1994; Braaten and Fuller, 2003) and four males and one female pallid sturgeon were 

documented bypassing the dam in 2014 by way of the natural side channel (Mike Backes, written 

commun., 2014). Currently, there is no evidence of recruitment upstream from Intake Dam. 

Downstream migration of juveniles or adults through reservoirs and dams is possible; 92 out of 3,721 

stocked fish recaptured in the Lower Missouri River downstream from Gavins Point Dam were 

originally stocked upstream from Gavins Point Dam (Steffensen and Huenemann, 2014). 

In addition to fragmentation exerted by the main stem reservoirs, the Lower Missouri and 

Middle Mississippi Rivers have substantial spatial variation associated with channel network structure 

(locations of tributaries), variable channelization and engineering, and locations of point sources of 

water-quality change (DeLonay and others, in revision). It has been hypothesized that variable 

physical and chemical habitat conditions along the Lower Missouri River may influence aggregation, 

spawning site selection, downstream dispersal of free-embryo larvae, and retention of early life stages. 

The CEMs presented here recognize the significant physical and biological differences between 

the upper river and the lower river. Additional sources of spatial variation occur within these areas, 

and will be addressed in management hypotheses, but the present level of analysis is limited to 

19 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

comparing the upper and lower-rivers. The upper river (Upper Missouri and Yellowstone Rivers) is 

characterized by a distinct genetic group of fish whose reproductive range is constrained by Fort Peck 

Dam, Vandalia Dam on the Milk River, Intake Dam on the Yellowstone River (to some extent), and 

the headwaters of Lake Sakakawea. It has been hypothesized that dispersal distances have been 

reduced because of migration impediments at Fort Peck Dam, Vandalia Dam, or Intake Dam, resulting 

in insufficient distance for ontogenetic development of free embryos to the endogenously feeding 

larval stage and that conditions in reservoirs are not suitable for survival of free embryos (Kynard and 

others, 2007; Braaten and others, 2012; Guy and others, 2015). This hypothesis is supported by the 

lack of recruitment in the Yellowstone and Upper Missouri Rivers (U.S. Fish and Wildlife Service, 

2000). In addition, the flow, temperature regime, and floodplain connectivity of the Upper Missouri 

River are strongly affected by releases from Fort Peck Dam. The releases from Fort Peck Dam result 

in decreases in water temperature in the spring and summer of about 2-3 degrees Celsius compared to 

the Yellowstone River, measured just upstream from the confluence (DeLonay and others, in revision). 

The lower river, downstream from Gavins Point Dam, differs significantly in several respects, 

including having genetically different groups of pallid sturgeon, and differences in alteration of the 

flow regime, temperature regime, water quality, channel morphology, and longitudinal and lateral 

connectivity. The flow regime from Gavins Point Dam results from system operations to serve 

multiple purposes including navigation, hydropower, flood control, recreation, and endangered species 

purposes. Because Lewis and Clark Lake, formed by Gavins Point Dam, is relatively small and 

shallow compared to other Missouri River main stem reservoirs, water residence times are short and 

river flows downstream from the dam do not show the decreased temperatures observed downstream 

from Fort Peck Dam; instead, water temperature tracks closely with air temperature in the spring-fall 

time period (DeLonay and others, in revision). The extent of channel engineering is very different on 

the Lower Missouri River compared to the upper river. The first 59 miles downstream from Gavins 

Point Dam (at river mile 811 upstream from the Mississippi River) has complex channel morphology 

and diverse habitats despite being affected by extremely low sediment transport, channel incision, low 

turbidity, and approximately 33 percent bank stabilization. From river mile 753 to the confluence with 

the Mississippi River (river mile 0), the river is channelized for stability and maintenance of a 

navigation channel. Agricultural runoff and point discharges from industrial and municipal water 

treatment facilities potentially contribute to water-quality stressors in this section of river (U.S. Fish 

and Wildlife Service, 2014). Unlike the upper river, downstream dispersal distance for juvenile fish is 

essentially unlimited as fish may disperse into the Middle Mississippi River. What is unknown is 

whether the channelized system on the Lower Missouri River allows free embryos to be retained in 

suitable habitat before reaching starvation, or whether sites amenable to retention occur and will allow 

for growth and recruitment to older stages. 

Although separate consideration of the upper and lower rivers is considered useful at this point 

in the analysis, we recognize that further spatial subdivisions of the upper and lower systems may be 

necessary as priority hypotheses are developed. Separate models may need to be developed for the 

Yellowstone and Upper Missouri Rivers, for example, or separate spatially explicit models may need 

to be developed to account for the punctuated gradient of environmental conditions downstream from 

Gavins Point Dam. A particularly important question is whether the Lower Missouri River should be 

considered as a single population of pallid sturgeon or should be divided into specific sub populations 

that use different parts of the river in their reproductive ranges. 

Inter-reservoir reaches fit generally within these CEMs, but they have not been emphasized 

because cold, clear water and peaking flows in inter-reservoir reaches are generally inconsistent with 

the highly turbid, warm water conditions under which the fish evolved (U.S. Fish and Wildlife 

Service, 2014). Additional spatial detail, including the role of inter-reservoir reaches, will be 

addressed in a later phase of the prioritization process. 20 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Descriptions of Component Models 

The following sections describe the specific component models with an emphasis on 

identifying the main hypotheses that are illustrated in the models. The models are presented 

graphically in the appendix and hypotheses thought to be important to survival probabilities (solid 

arrows) are labeled on the component CEMs and are cross-referenced in table 2. It should be noted 

that hypotheses are further refined and tested in subsequent steps of the EA process. Furthermore, 

some apparent inconsistencies between upper river and lower river hypotheses may be due to actual 

differences in conditions, and some may be due to the differences in expert opinions of the members of 

the two workshop groups. 

Upper River 

Upper river models share common characteristics on the left hand side of the CEM diagrams 

(appendix figures A1 through A5). In general, management actions involving reservoir engineering 

and operations are thought to have greater importance, whereas actions related to channel 

management and restoration are judged to have less importance, relative to the lower river. 

Pre-Spawn and Spawning Adults 

Pre-spawning adults are fish in the final stages of preparing for spawning. Spawning adults 

refers to female fish with oocytes that can be released and fertilized and male fish with flowing milt. 

The component model for this life stage is especially complex in depicting potential linkages from 

secondary ecological factors to primary biotic responses because of the many ways that reproductive 

behaviors may be linked to environmental variables. The end point for this CEM is viable embryos, 

which will result from successful spawn and fertilization. 

Removal as a direct source of mortality is considered relatively certain and important and 

reflects concerns about losses to this small segment of the overall population that could result from 

poaching, impingement, entrainment, bycatch mortality in permitted fisheries, and removal of fish for 

broodstock use in hatcheries. Factors related to reproductive synchrony are shown as uncertain and 

important. In particular, characterization of the link from spawning site selection to survival to viable 

embryos arises from emerging telemetry information that documents non-systematic patterns of 

upstream and downstream migration behavior, suggesting a search for suitable spawning sites with 

suitable mates (Fuller and others, 2008; DeLonay and others, in revision). Migration is considered to 

be of moderate importance and moderate uncertainty, reflecting an analysis of telemetry data that 

shows that pallid sturgeon optimize migration pathways to minimize energy expenditures (Spindler 

and others, 2009; McElroy and others, 2012; DeLonay and others, in revision). Few hybrids have 

been collected in the upper river, so hybridization is thought to be relatively unimportant. Growth 

and condition factors in this life stage include gonad condition (fecundity). Growth and condition are 

linked with importance and substantial uncertainty of survival to viable embryos, reflecting the 

hypothesis that productivity and food availability may be important for fecundity. 

A variety of secondary ecological factors link with highest importance and moderate 

uncertainty to reproductive behaviors. These represent competing (or inter-related) hypotheses for 

how environmental conditions affect reproductive behaviors and result in synchrony (that is, males 

and females in the same reproductive condition at the same time and in a location that is amenable to 

spawning and fertilization). 

21 
 

Table 2. Candidate working set of biologically dominant hypotheses. 

Life stage, Appendix

location Process category Label Hypothesis 

AU1a Barriers to upstream migration prevent access to functional spawning 

sites with supportive hydraulics and substrate, thereby decreasing 

Reproductive behavior and probability of producing viable embryos. 

synchrony AU1b Hydrology-related events are inadequate to cue aggregation of 

reproductive adults, thereby decreasing probability of mates to find 

one another. 

AU2a Take of pre-spawn adults through removal or other mechanisms Direct mortality increases direct mortality. 

AU3a Population augmentation has increased numbers of conspecifics, 

increasing competition for food resources in a fragmented system with Growth and condition decreased productivity, thereby decreasing growth, condition, and 

fecundity (pertains to Upper Missouri River). 

Developing embryos Pre-spawn and spawning adults 

Lower river Upper river Upper river Lower river 

AL1a	 Habitat alterations have decreased separation of reproductive shovelnose 

(Scaphirhynchus platorynchus) and pallid sturgeon(Scaphirhynchus albus) 

in space and time, thereby increasing hybridization. 

AL1b Habitat alterations have decreased availability of functional spawning 

habitat while also increasing availability of attractive, sub-optimal Reproductive behavior and spawning habitat, thereby decreasing probability of mates finding one synchrony another. 

AL1c Hydrology-related events are inadequate to cue aggregation of 

reproductive adults, thereby decreasing probability of mates to find one 

another. 

AL2a	 Channelization and changes in flow regime have decreased food 

availability, which results in decreased growth, condition, and fecundity. 

Growth and condition AL2b Channelization and changes in flow regime have increased velocities and 

decreased habitat suitability and complexity, resulting in decreased 

growth, condition, and fecundity. 

EU1b Hypolimnetic releases of cold water have increased embryo incubation 

time, which results in increased predation prior to hatch. 

Direct mortality EU1b Decreased turbidity has increased efficacy of pre dators and predation 

prior to hatch (pertains to Upper Missouri River). 

EU1c Increased numbers of predators have increased predation prior to hatch. 

EL1a Decreased turbidity has increased efficacy of predators and predation 

prior to hatch. 

Direct mortality EL1b Increased numbers of int r oduced or invasive predators have increased 

predation prior to hatch. 

EL1c Channelization and changed flow regimes have increased scour and 

sediment deposition in embryo incubation areas resulting in increases 

in direct mortality of developing embryos by detachment, entrainment, 

or sedimentation (by crushing or smothering). 

22 
 

 

Table 2 . Candidate working set of biologically dominant hypotheses. -Continued

Life stage, 

location Process category Label Hypothesis 

FU1a	 Hypolimnetic releases of cold water have increased embryo incubation time 

which results in increased predation prior to settling. 

FU1b	 Reservoirs have decreased turbidity, resulting in increased efficacy of 

predators and increased direct mortality from predation prior to settling 

(pertains to Upper Missouri River). 

FU1c	 Increased numbers of predators has increased predation prior to settling 

Direct mortality (pertains to Upper Missouri River). 

FU1d Barriers to upstream migration limit available downstream dispersal distance 

such that dispersing free embryos settle in unsuitable habitats in the 

headwaters of downstream reservoirs, which increases direct mortality. 

FU1e Barriers to upstream migration limit available downstream dispersal distance 

such that dispersing free embryos settle in habitats that are not suitable for 

first feeding, thereby increasing direct mortality. 

Growth and condition FU2a	 Changes in flow regime, water quality, and (or) local habitat in settling areas 

have decreased the prey base for first feeding, decreasing growth, condition, 

and survival. 

Free embryos 

Lower river Upper river

FL1a Channelization has decreased post-hatch refugia in substrate interstices 

resulting in increased direct mortality from predation. 

FL1b Reservoirs have decreased turbidity, resulting in increased efficacy of predators 

Direct mortality and increased direct mortality from predation prior to settling. 

FL1c Channelization has decreased suitable hydraulics to intercept and retain 

drifting free embryos, resulting in increased direct mortality by starvation 

and inability to transition to first feeding. 

FL2a Channelization has decreased supportive habitat conditions for first feeding 

Growth and condition (increased velocities, lack of habitat complexity), decreasing growth, 

condition, and survival. 

FL2b Changes in flow regime, water quality, and/or channel complexity in settling 

areas result in lack of suitable food for first feeding and decreases to growth, 

condition, and survival. 

23 
 

 

 

 

 

Table 2. Candidate working set of biologically dominant hypotheses.-Continued

Life stage, 

location 

Appendix 

Process category label Hypothesis 

Juveniles Exogenously feeding larvae 

Lower river Upper river Lower river Upper river 

Direct mortality 

Growth and condition 

Direct mortality 

Growth and condition 

LU1a Reservoirs have decreased turbidity, resulting in increase d efficacy ofpredators 

and increased direct mortality from predation. 

LU1b Increased numbers of introduced or invasive predators have 

increasedpredation. 

LU1c Reservoirs have created unsuitable habitat conditions in headwaters wheremany 

free embryos settle, resulting in increased direct mortality. 

LU2a	 In areas upstream from reservoir headwaters, increased summer reservoir 

releases result in increased velocities, decreases in supportive habitat, and 

decreases in growth, condition, and survival. 

LU2b Changes in flow regime have decreased productivity of suitable foods, decreasing 

growth, condition, and survival. 

LL1a Reservoirs have decreased turbidity, resulting in increased efficacy of predators 

and increased direct mortality from predation. 

LL1b Increased numbers of introduced or invasive predators increase predation 

LL1c Changes in flow regime and channelization have resulted in increased quality of 

physical habitat for predators, resulting in increased predation. 

LL2a Changes in flow regime and channelization have resulted in increased 

velocities, a decrease in supportive channel complexity, and decreases 

growth, condition, and survival. in 

LL2b Changes in flow regime and channelization have resulted in decreased 

productivity of suitable food, which decreases growth, condition, and survival. 

JU1a Reservoir releases have altered flow and temperature regimes, increasing 

bioenergetic demands and decreasing growth, condition, and survival. 

JU1b Reservoir releases have altered flow and temperature regimes, decreasing 

productivity and food availability, and resulting in decreases in growth, 

Growth and condition condition, and survival. 

JU1c Population augmentation has increased numbers of pallid sturgeon beyond 

what current (2014) habitats can support, increasing competition for food 

resources in a fragmented system with decreased productivity, thereby 

decreasing growth, condition, and survival. 

JL1a Reservoir releases have decreased flow variation, resulting in decreased 

productivity and food availability, and decreases in growth, condition, and 

survival. 

Growth and condition 

JL1b	 Channelization has decreased channel complexity, resulting in decreased 

productivity and food availability, and decreases in growth, condition, and 

survival.

 Physical habitat availability is dominantly a spatial issue controlled by local hydraulics and substrate, 

as well as longitudinal connectivity to allow habitats to be accessed. Water-quality factors also have a 

strong temporal component because they may act to cue or synchronize physiology and behaviors in 

time (DeLonay and others, 2009; DeLonay and others, in revision). Flow regime is shown as an 

important factor affecting physical habitat and water quality dynamics, as is water-quality regime 

(including temperature). The potential effect of flow regime on migration and aggregation behaviors 

is shown as filtered through physical habitat and water-quality dynamics, indicating the belief that the 

fish experience flow regime through some combination of hydraulics, temperature, or turbidity. 

24 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Potential management actions that link to important primary ecological factors are reservoir 

operating rules, passage structures, water-quality structures, and dam locations. The strength of the 

linkages of management and restoration actions to primary ecological factors like flow and waterquality regimes is confounded somewhat by the fact that Upper Missouri and Yellowstone River 

segments are combined in these models. In the Yellowstone River, the flow regime is nearly natural 

and unmanaged, whereas in the Upper Missouri River, the flow and temperature regimes are highly 

affected by Fort Peck Dam; therefore, operating rules and water-quality structures do not apply on the 

Yellowstone River but may be considered on the Upper Missouri River. Passage structures apply 

mainly to the Yellowstone River for facilitation of migration over or around Intake Dam (and 

potentially another low-head dam at Forsyth, Montana); passage would only be considered relevant to 

the Upper Missouri River if migration up the Milk River or access to Fort Peck Lake was considered 

ecologically useful for pallid sturgeon. Downstream from the Upper Missouri/Yellowstone River, the 

headwaters of Lake Sakakawea are hypothesized to be unsupportive of early life stages because of 

unsuitable water-quality conditions and possible predation, relying on extrapolation of results from the 

headwaters of Fort Peck Dam(Guy and others, in press). Locations of dams are listed as a 

management action in relation to historical decisions to locate dams and to future decisions for dam 

locations or removals (however improbable). 

Developing Embryos 

Developing embryos refers to fertilized eggs prior to hatching. The temporal duration of the 

life stage is inversely related to temperature and lasts generally 5-8 days. The end stage of this CEM is 

the hatching of free embryos. 

Survival to hatch is associated with processes the may impose direct mortality. Linkages from 

water-quality factors to growth and condition refer mainly to water temperature and dissolved oxygen 

around developing embryos. Direct mortality of embryos through contaminant toxicity is thought to 

have low importance and moderate uncertainty. Although there is historical documentation of organicchemical contaminant accumulation in eggs, laboratory studies indicate low mortality (Buckler, 2011; 

Missouri Department of Health and Senior Services, 2011). Exposure to industrial chemicals and 

pesticides also has been low in the upper river segments. Early detections of metals, PCBs, DDT, and 

organochlorine compounds in tissue samples from pallid sturgeon in the upper river (Ruelle and 

Kennlyne, 1993) have not been replicated in the last 20 years, indicating that contaminant exposure 

may have decreased with time. Metals associated with mining may be a significant source of 

contamination (Zelt and others, 1999). Linkages to reproductive behaviors at this life stage are 

included to indicate the role of hydraulics in determining whether fertilization occurs and whether 

embryos end up in the right type of substrate and velocity field where they can incubate. 

Egg predation is shown as an important, moderately uncertain linkage from the aquatic 

community to survival. Processes of scour and sedimentation are shown as moderately important, 

highly uncertain links from physical habitat conditions to survival. Linkages from primary ecological 

factors to secondary factors are similar to the pre-spawning and spawning adult. 

Free Embryos 

The free embryo life stage is defined as a developing fish between hatch and first feeding. 

During this life stage the free embryo is no longer protected by the chorion and it relies on its yolk 

reserves to continue development. The life stage may last 7–12 or more days, depending on 

temperature (Kynard and others, 2002, 2007; Braaten and others, 2008, 2012). Field and laboratory 

studies continue to address key questions regarding behavior, downstream dispersal, and survival 

probabilities of sturgeon free embryos after hatch. Recent studies 

25 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

on other sturgeon species have questioned whether drift commences immediately upon hatch or 

whether instead sturgeon free embryos are more likely to survive if they remain in substrate interstices 

near the incubation site for some period of time, thereby allowing for more growth and improved 

swimming ability before initiating downstream dispersal and first feeding (McAdam, 2011; Crossman 

and Hildebrand, 2012; DeLonay and others, in revision). 

 Two hypotheses are thought to have high importance for survival of free embryos to the 

exogenously feeding larva stage. The first of these hypotheses addresses what happens if the free 

embryo is transported into lethal water-quality conditions, which has been suggested for free embryos 

that are transported into Lake Sakakawea (Braaten and others, 2012; Guy and others, in press). A 

related hypothesis links physical habitat to survival through growth and condition. This hypothesis 

addresses the situation when a free embryo is retained in a physically supporting habitat but one that 

lacks sufficient food quantity or quality, and the free embryo subsequently starves. 

Two additional hypotheses rated as important depend in part on physical habitat and the aquatic 

community. Predators in the aquatic community are linked to direct mortality. Dispersing free 

embryos have poor predator avoidance capabilities and have an elevated risk of encountering a 

predator during the dispersal phase. Similarly, competition arises from elements of the aquatic 

community that would seek the same food sources as the free embryo when it transitions to first 

feeding. 

Direct mortality by removal is also shown as a hypothesis to address the situation where 

free embryos are impinged on screens (for example, in municipal, industrial, or irrigation 

diversions) or otherwise entrained into water diversions. The importance of this process is 

currently thought to be relatively low, although the uncertainty is high. 

Hypothesized linkages to management actions for this life stage are complex and, similar to 

previously discussed life stages, the hypotheses mix Upper Missouri and Yellowstone Rivers contexts. 

Reservoir operations on the Missouri River are strongly linked to flow regime, which may propagate 

through many secondary ecology factors. In particular, water velocities and consequent free-embryo 

transport rates can be affected by reservoir releases with high discharges resulting in generally high 

velocities and greater probability that free embryos would be transported into Lake Sakakawea. 

Reservoir operations or implementation of structures that could result in release of warmer water could 

increase developmental rate resulting in earlier transition to exogenously feeding larvae and shorter 

drift distances. Fish passage at Intake Diversion Dam on the Yellowstone River could increase 

available drift distance by allowing sturgeon to spawn farther upstream, if suitable spawning habitat 

exists. Optimization of spawning patches to increase retention of newly hatched free embryos or 

reconstruction of channel morphology to enhance interception of drifting free embryos could serve to 

decrease time and distance in the drifting stage, in either river. Finally, draw-down of Lake Sakakawea 

has the potential to create a longer drift distance and improve retention habitat by increasing the length 

of lotic habitat within the Upper Missouri River. 

Exogenously Feeding Larvae 

Exogenously feeding larvae are developing, feeding fish. This stage begins with first feeding 

and ends when fish transition to juvenile stage with a full complement of rays in all fins and the 

allometric relation between length and weight stabilizes. This stage usually completes before the first 

winter. 

Predation is hypothesized to be an important component of natural mortality but with high 

uncertainty. Predation on this stage has been documented for other sturgeon species (Gadomski and 

Parsley, 2005). However, predation of larval pallid sturgeon has been shown in laboratory settings to 

be low when alternative prey is available, and insensitive to turbidity within a low to moderate range 

26 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

relative to post-impoundment turbidities (French and others, 2010; Blevins, 2011; French and others, 

2013a). Predation is linked dominantly to the aquatic community but, of course, the aquatic 

community is linked in complex ways to various combinations of primary and secondary ecological 

factors. 

Survival is also strongly linked to growth and condition through habitat suitability, food 

availability, and extent of competition. These growth and condition factors are similarly linked in 

complex ways to physical habitat, water quality, and aquatic community factors; the conceptual 

ecological model captures but does not disentangle these inter-relating hypotheses. 

Removal through impingement or entrainment is also possible at this age, but no studies have 

addressed this in the Missouri River so uncertainty is high (Gutreuter and others, 2003). 

Lethal water quality (anoxia) is retained as an important, but uncertain, hypothesis for this life 

stage based on the premise that dispersing free embryos may transition to exogenously feeding 

embryos after being transported into the headwaters of Lake Sakakawea. 

Management actions that could influence survival are similar to the free embryo life stage, 

except there is more emphasis on actions that would increase food availability. Changes in flow and 

water-quality regimes (especially temperature) may increase or diminish physical habitat, water 

quality, and the aquatic community, with consequence for bioenergetics, growth, and condition that 

will allow larvae and juveniles to survive the winter. Because the larvae are feeding dominantly on 

zooplankton and invertebrates at this stage, conditions that increase these food types may be especially 

important. Overbank flows (floodplain or lateral connectivity) are hypothesized to be critical for 

stimulating food production on flood plains, for flushing food resources into the main stem habitats 

occupied by pallid sturgeon, and perhaps for increased retention of larvae (Bayley, 1991; Coutant, 

2004; Thorp and others, 2006), although uncertainty is high because of the challenges of 

demonstrating the linkages among overbank flows, food resources, and occupancy of young fish. 

Implicit in the hypothesis is the idea that near-natural channel morphology in the upper river indicates 

that quantity and quality of in-channel habitat should not be limiting. Increased overbank flows can be 

accomplished by manipulating reservoir releases to increase flooding by removing engineered levees 

and by engineering channels to match the new hydrologic regime. These actions would involve socialeconomic tradeoffs such as loss of agricultural revenue. Because few levees exist along the 

Yellowstone and Upper Missouri Rivers, levee removal is not envisioned as a relevant action (under 

channel reconfiguration). Increased fish passage would result in greater overall area and food 

available to the fish population, whereas water-quality management would be linked to increased 

temperatures and productivity. 

Juveniles 

The juvenile life stage extends from when a fish has a full complement of fin rays to when it 

enters its first reproductive cycle, generally about 750 millimeters fork length (Albers and others, 

2013; Steffensen and others, 2013b). During this period, a subadult stage may be defined when the 

fish’s diet shifts from predominantly invertebrates to predominantly fish (Gerrity and others, 2006; 

Grohs and others, 2009; French and others, 2013b); however, the current conceptual ecological model 

groups these two life stages together pending further information indicating this transition is crucial to 

survival. 

Emphasis during this life stage is on hypotheses relating survival to growth and condition, 

resulting dominantly from productivity of the aquatic community and water temperature (Kappenman 

and others, 2009). Physical habitat is thought to have a secondary effect, although similar to the 

larval life stage, productivity is thought to be linked to flow regime and channel morphology factors 

that stimulate food production and help flush food into pallid sturgeon habitats. Competition, 

predation, disease, and removal through entrainment and removal are also hypothesized to be 

important and varying from moderately to highly uncertain. 

27 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Similar to the larval life stage, management actions envisioned to increase food resources 

would emphasize flow releases designed to connect to overbank areas or removal of impediments to 

overbank flooding to increase food production. There is uncertainty about the current production of 

forage in channel habitats. Increased fish passage would result in greater overall area and food 

available to the fish population whereas water-quality management would be linked to water 

temperatures and increased productivity. 

Lower River 

In comparison to the upper river, the lower river introduces an additional management 

opportunity in restoration of channel configurations (Jacobson and Galat, 2006). Also, the severity of 

flow-regime alteration diminishes in the downstream direction (Galat and Lipkin, 2000; Pegg and 

others, 2003), so reservoir management may assume less importance for some life stages in some parts 

of the lower river. 

Definitions of life stages for the lower river models (figs. A6-A10) are identical to the 

upper rivers (figs. A1-A5) definitions. 

Pre-Spawn and Spawning Adults 

One hypothesis that was ranked important and relatively certain for this life stage relates 

survival to growth and condition resulting from a combination of physical habitat, water-quality 

dynamics, and aquatic community composition. Key linkages are hypothesized to be from physical 

habitat and temperature to habitat suitability, indicating a hypothesis about fundamental bioenergetics 

controls. A less certain linkage is from the aquatic community to food availability, indicating the 

potential for lack of prey fish to limit reproductive fitness of adult pallid sturgeon. Hybridization is 

also indicated as an important and relatively certain linkage from congenerics in the aquatic 

community (shovelnose sturgeon) to decreased probability of pallid sturgeon survival. 

A variety of physical and water-quality factors are linked to reproductive behaviors and 

synchrony, indicating the strong and complex relations between physical and chemical habitat and 

reproductive behaviors at this life stage. Among these linkages is the hypothesis that reproductive 

aggregations and probabilities of suitable mates finding each other have been diminished by overprovision of hard, coarse substrate in bank revetment and channel-training structures (DeLonay and 

others, in revision). The premise for this hypothesis is that the small remaining reproductive 

population is too spread out to find suitable mates when females are ready to spawn, resulting in atresia 

or increased hybridization with shovelnose sturgeon. Spawning success could be increased by 

increasing numbers of reproductive adults, increasing quality of spawning patches to attract more of 

the existing population, or both. A related hypothesis that channelization has increased migratory 

energy expenditures, and thereby decreased reproductive fitness and the probability that mates can find 

each other, has not been supported by recent assessments of energy requirements of migratory 

pathways (McElroy and others, 2012). The result of multiple effects on survival of gametes is shown 

as relatively uncertain because of the competing and possibly inter-related hypotheses. Removal of 

pre-spawning and spawning adults has been assigned moderate importance and low uncertainty. 

The lower river component models all show a greater role for channel morphology 

management compared to the upper river because of the extent of past alteration and the potential for 

reconfiguration of channel morphology as a restorative action. Channel morphology influences this 

life stage according to two dominant hypotheses. One hypothesis holds that adult reproductive fitness 

relates to growth and condition, indicated by food availability. Food availability, in turn, would be 

linked to habitat suitability for prey species, which could be increased through channel 

28 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

reconfigurations and flow management. Increased food would be linked to increased pallid sturgeon 

reproductive fitness, gamete quality, and embryo viability. The second hypothesis is that construction 

of more suitable and attractive spawning habitat in fewer locations would be sufficient to attract 

aggregations of reproductive pallid sturgeon. 

Reservoir flow management actions link to flow regime and physical habitat, as well as directly 

to reproductive behaviors and synchrony. Managed flow regimes are shown interacting strongly with 

channel morphology to determine physical habitat dynamics, and also acting as environmental cues 

that are hypothesized to help synchronize reproductive fish. Reproductive cues are hypothesized to be 

important but moderately uncertain, in part because they can arise through direct changes in discharge 

or uncertain combinations of discharge, temperature, turbidity, or other flow-related variables. 

Management actions related to passage structures have been hypothesized to influence 

longitudinal connectivity with the potential to provide greater access to suitable spawning substrates. 

Rivers with impediments to passage include the Kansas and Osage Rivers, and there is potential that 

historical spawning areas on the main stem have been inundated upstream from Gavins Point Dam. 

Included in water quality structures are potential management actions to pass sediment through or 

around reservoirs. These actions would increase turbidity, result in decreased competition, and 

potentially increase reproductive fitness. 

Developing Embryos 

Dominant hypotheses for limited survival at the developing embryo stage hold that (1) 

spawning site hydraulics are not suitable for gamete placement and fertilization, and (or) that (2) 

spawning sites are susceptible to scour and deposition processes that either dislodge or bury incubating 

embryos, resulting in direct mortality. These hypotheses are supported by precise mapping of 

spawning locations on the Lower Missouri River that indicate spawning in zones of active sand 

transport in deep, fast, and turbulent water on outside bends (DeLonay and others, in revision), where 

fertilization may be problematic and scour and deposition threaten eggs during incubation. Predation 

is also given high importance and moderate uncertainty as a source of mortality based on studies of egg 

predation in other sturgeon species. Predation on pallid sturgeon embryos likely occurs but has not 

been documented. The effects of water quality on growth or lethal conditions for embryos, and the 

potential roles of disease on survival probabilities have relatively low importance but high uncertainty. 

The role of contaminants in decreasing embryo survival is given somewhat greater importance and has 

lower uncertainty because of the historically documented contaminant accumulation of industrial 

organic chemicals in eggs compared to recent laboratory studies indicating only slightly decreased 

embryo survival with increasing exposure to persistent organic chemicals (Buckler, 2011; Missouri 

Department of Health and Senior Services, 2011). 

The dominant MRRP management action hypothesized for this life stage are channel 

reconfigurations that serve to decrease scour or sedimentation of eggs. Flow-regime management 

could also be useful in limiting scour and sedimentation in some cases but would be less specific than 

channel reconfiguration. Moreover, flow-regime management would have decreasing influence 

downstream because the effects of reservoir flow releases decrease in the downstream direction. 

Free Embryos 

The most important, but relatively uncertain, hypothesis relating to survival of free embryos is 

shown as the linkage from physical and chemical habitat to growth and condition. Increased growth 

and condition of free embryos are expected to result in increased survival when the free embryos can 

access suitable habitats characterized by hydraulics that are favorable for retention and water quality. 

The availability of sufficient, high-quality food is also linked as part of habitat suitability for growth 

and condition 29 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

when the free embryo transitions to exogenous feeding. Additional hypotheses of moderate importance 

link physical and chemical habitat to survival probability through successful first feeding and lethal 

water quality (that is, high temperatures or low dissolved oxygen). The successful first feeding 

hypothesis relates to hydraulic conditions that allow drifting free embryos to “settle out” and be 

retained in supporting habitats, or hydraulic conditions that provide forage to areas where free embryos 

first require food. The lethal water quality hypothesis relates to the potential lethal effects of high 

water temperature and low dissolved oxygen that can develop at times in the Lower Missouri River 

during the summer (Blevins, 2011), and might be more prevalent in slow, deep water in wing-dike 

complexes. In addition, predation on free embryos is depicted as important but highly uncertain. 

The primary ecological factor for this life stage is the interaction of channel morphology and 

flow regime that determines physical habitat dynamics and influences water-quality dynamics in 

drifting and retention habitats. The main management actions are (1) channel reconfigurations that 

would increase hydraulic diversity, encourage recirculating eddies to increase retention (interception 

habitats), and increase hydraulic flow resistance, thereby decreasing mean-channel velocities; and (2) 

flow management actions that would influence transport of free embryos by increasing or decreasing 

mean velocities. Both management actions depend, however, on an understanding that retention in 

particular locations would increase growth and condition relative to retention in other areas. This 

logic assumes that management actions to create retention areas account for the possibility of 

increased predation by native or non-native species and poor water quality. Management actions 

affecting water-quality regime are limited because sections of the river that would be directly 

affected by operational changes at Gavins Point Dam are limited in extent and many sources of 

water-quality stressors exist downstream that are beyond USACE management authorities. The 

possibility exists that channel reconfiguration could be designed to increase exchange between the 

main channel and marginal habitats, thereby minimizing stagnant water behind wing dikes where 

elevated temperatures and diminished dissolved oxygen may be likely. 

Exogenously Feeding Larvae 

The two important linkages identified for survival through the first winter are predation and 

growth and condition related to habitat suitability and food availability. The presence and efficacy of 

predators are linked to dynamics of predators’ habitats (linkage from physical habitat to aquatic 

community) as well as habitats occupied by the larval pallid sturgeon. Habitat suitability is linked to 

hydraulics, temperature, and dissolved oxygen, which determine conditions conducive to growth. A 

moderately important, moderately uncertain linkage was identified between productivity of the aquatic 

community and food availability; assignment of moderate importance to this linkage is based on a lack 

of evidence for food availability constraints, although theory would support the idea that food 

availability and growth are critical for survival through the first winter (Post and Parkinson, 2001; 

Wildhaber and others, 2007; Wildhaber and others, 2011). 

Management actions to increase survival at this stage that would propagate through relevant 

ecological factors are channel reconfigurations and reservoir operations and engineering. Channel 

reconfigurations have been implemented as the SWH creation RPA on the Lower Missouri River since 

the 2003 Biological Opinion. The SWH effort is reflected in this model as one approach to channel 

reconfiguration actions that alter channel morphology but also interact in complex ways with flow 

regime, sediment regime, and water quality to affect physical habitat dynamics, water-quality 

dynamics, and the aquatic community. The complexity of linkages and attendant uncertainties evident 

in this model underscore the understanding that although loss of shallow, slow-water habitat and 

habitat diversity has been well documented (Funk and Robinson, 1974; Hallberg and others, 1979; 

Hesse and Sheets, 1993; Jacobson and Galat, 2006), the specific mechanisms by which channel 

30 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

reconfiguration may support pallid sturgeon populations are poorly understood and have only recently 

begun to be a focus of descriptive field studies. Initial work to understand the distribution of 

Scaphirhynchus sturgeon during the latter part of the early life stage reflected in this CEM has 

demonstrated use of relatively fast velocity (that is, 0.5-0.7 meters per second bottom velocity) 

habitats, such as large channel sandbars and rootless dikes, that were generally adjacent to the river 

thalweg, and lack of use of habitats that had slow velocity or were largely disconnected from the 

thalweg (Ridenour and others, 2011). Moreover, channel configurations to support growth and 

condition of exogenously feeding larvae would be most effective when matched with locations to 

which free embryos and exogenously feeding larvae will disperse. 

Flow management interacts with channel configuration to determine hydraulics, and to some 

extent, water quality in occupied habitats. Flow management also has the potential to create overbank 

flows that would connect with flood plains, boost primary and secondary productivity, and flush food 

resources into habitats occupied by pallid sturgeon (Bayley, 1991). The general hypothesis that 

periodic connection of channels with flood plains is necessary to spur system productivity is prominent 

in the large-river scientific literature (Junk and others, 1989; Sparks, 1995; Poff and others, 1997; 

Sparks and others, 1998; Tockner and others, 2000). In the CEM exercise, however, the hypothesis 

that increased food would increase survival at this stage was assigned only moderate importance. For 

the hypothesis to have greater support, data would need to demonstrate that: (1) food is a limiting 

factor in growth and condition of pallid sturgeon, (2) in-channel reconfiguration management actions 

are insufficient to reduce food limitation, (3) sufficient non-leveed riparian lands exist for flow pulses 

to be effective, and (4) floodplain lands can be connected with adequate magnitude, duration, and 

timing for discharges. The desire for private and public levee protection is much more prevalent on the 

Lower Missouri River compared to the upper river, but restoration of as much as 80,000 acres of 

floodplain conservation lands has been planned on the lower river (U.S. Army Corps of Engineers, 

2003), which could provide for effective floodplain connectivity depending on hydrology and local 

channel condition (Jacobson and others, 2011). Sediment management to increase downstream 

turbidity is also hypothesized to decrease competition and predation (National Research Council, 

2011). All management actions involving reservoir engineering and operations on the Lower Missouri 

River occur within the spatial context that magnitude of any action at Gavins Point Dam diminishes in 

relative importance as downstream tributaries affect fluxes of water, sediment, and water-quality 

constituents. 

Juveniles 

The dominant linkages to survival to adult are related to habitat suitability and food 

availability, in their importance to growth and condition (Spindler and others, 2012). Habitat 

suitability is strongly linked to hydraulic conditions that would support energy efficiency, and to 

hydraulics and aquatic community composition that would support food supply. Water temperature is 

also hypothesized to have a role in regulating growth and condition because it has been documented 

that optimal juvenile growth occurs at 28 degrees Celsius and temperatures greater than 35 degrees 

Celsius may be lethal (Chipps and others, 2008). Competition is recognized as an important and 

uncertain factor influencing growth and condition. Predation, disease, and removal (poaching, 

entrainment, or impingement) are recognized as moderately important contributors to mortality with 

varying uncertainty. 

Potential management actions that would propagate to affect growth and condition of juveniles 

are similar to those discussed for larval fish. Channel reconfigurations are hypothesized to interact 

with flow regime, sediment regime, and water-quality characteristics to affect physical habitat, 

chemical habitat, and the aquatic community. A key difference may be the type of channel 

31 
 

 

 

 

configuration and associated habitats that would be most effective in supporting different food 

sources. A design that encourages organic matter retention and mud substrate may, for example, 

support invertebrate production that would benefit young juveniles. Another design might provide 

hydraulics and substrate that would support prey-fish production, which would be more important for 

older juveniles that have transitioned to a piscivory (Gerrity and others, 2006; Wildhaber and others, 

2011; French and others, 2013b). Hence, understanding this complex linkage may require increased 

understanding of the ecological factors that support prey populations (Ridenour and others, 2009). 

Channel configurations may also affect local water residence time and consequently temperature, and 

therefore may be designed to avoid lethal temperatures or optimize temperature for growth. 

Flow management actions are similar to those for larval fish. Flow management would interact 

with channel configuration to determine hydraulics, and affect in-channel and overbank water quality 

and aquatic community dynamics. Flows that connect the floodplain to channel habitats would boost 

primary and secondary productivity, and flush food resources into main stem habitats. Additional 

food in the form of invertebrates may support pallid sturgeon directly or indirectly through prey-fish 

populations. Management actions involving reservoir engineering and operations will diminish in 

relative importance as downstream tributaries affect fluxes of water, sediment, and water-quality 

constituents. 

Summary and Conclusions 

This report documents the process of developing and refining conceptual ecological models for 

linking management actions to pallid sturgeon (Scaphirhynchus albus) population dynamics in the 

Missouri River. The general form of the conceptual ecological models (CEMs), represented by a 

population-level model and component life-stage models, was determined in workshops held in the 

summer of 2013. Subsequently, the Missouri River Pallid Sturgeon Effects Analysis team designed a 

general hierarchical structure for the component models, refined the graphical structure, and reconciled 

variation among the components and between models developed for the upper river (Upper Missouri and 

Yellowstone Rivers) and the lower river (Missouri River downstream from Gavins Point Dam). 

Importance scores attributed to the relations between primary biotic characteristics and survival were used 

to define a candidate set of working dominant hypotheses that are likely to be relevant to pallid sturgeon 

population dynamics. 

The resulting CEMs are intended to be used as a foundation for adaptive management of pallid 

sturgeon populations in the Missouri River. The CEMs provide a structure for understanding and 

communicating complex abiotic and biotic processes in the Missouri River. In addition, the relations in the 

CEMs comprise a global set of hypotheses, which have the potential to explain some part of pallid sturgeon 

population dynamics. Although emphasis in the short term (2-5 years) will focus on relatively few specific 

hypotheses thought to be the most influential, the CEMs can be considered a reserve of hypotheses that can 

be revisited as needed if other hypotheses fail to explain observed population changes. 

32 
 

 

 

 

 

 

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Appendix 

Graphical presentations of conceptual ecological models by life stage and location. 

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