Grand Canyon Monitoring

and Research Center

Fiscal Year 2016 Annual Project Report

for the

Glen Canyon Dam

Adaptive Management Program
Contents

Introduction ......................................................................................................................................... 3

Project 2: Streamflow, Water Quality, and Sediment Transport in the Colorado River Ecosystem... 4

Project 3: Sandbars and Sediment Storage Dynamics: Long-term Monitoring and Research at the 

Site, Reach, and Ecosystem Scales ................................................................................................... 12

Project 4: Connectivity Along the Fluvial-Aeolian-Hillslope Continuum: Quantifying the Relative 

Important of River-Related Factors that Influence Upland Geomorphology and Archaeological Site 

Stability ............................................................................................................................................. 18

Project 5: Foodbase Monitoring and Research.................................................................................. 29

Project 6: Mainstem Colorado River Humpback Chub Aggregations and Fish Community 

Dynamics........................................................................................................................................... 37

Project 7: Population Ecology of Humpback Chub in and around the Little Colorado River.......... 47

Project 8: Experimental Actions to Increase Abundance and Distribution of Native Fishes in Grand 

Canyon............................................................................................................................................... 58

Project 9: Understanding the Factors Determining Recruitment, Population Size, Growth, and 

Movement of Rainbow Trout in Glen and Marble Canyons............................................................. 64

Project 10: Where does the Glen Canyon Dam Rainbow Trout Tailwater Fishery End? – Integrating 

Fish and Channel Mapping Data below Glen Canyon Dam ............................................................. 78

Project 11: Riparian Vegetation Monitoring and Analysis of Riparian Vegetation, Landform 

Change and Aquatic-Terrestrial Linkages to Faunal Communities.................................................. 82

Project 12: Changes in the Distribution and Abundance of Culturally-Important Plants in the 

Colorado River Ecosystem: A Pilot Study to Explore Relationships between Vegetation Change and 

Traditional Cultural Values............................................................................................................... 93

Project 13: Socioeconomic Monitoring and Research .................................................................... 101

Project 14: Geographic Information Systems (GIS) Services and Support .................................... 107

Project 15: Administration .............................................................................................................. 111

Project 1: Lake Powell and Glen Canyon Dam Release Water-Quality Monitoring...................... 113
3

Introduction

Following is the Grand Canyon Monitoring and Research Center’s (GCMRC) Fiscal Year (FY) 

2016 Annual Accomplishment Report. This report is prepared primarily for the Bureau of 

Reclamation to account for work conducted and products delivered in FY16 and to inform the 

Technical Work Group (TWG) of science support provided to the Glen Canyon Dam Adaptive 

Management Program (GCDAMP). It includes a summary of accomplishments, shortcomings, and 

recommendations related to projects included in GCMRC’s FY16 Work Plan for the GCDAMP1.

The report also includes budget summaries for each project as well as a separate budget for logistics 

operations. In addition to project costs, budgets show funds carried forward from FY15, shortfalls 

in funding due to lower than projected Consumer Price Index values, and funds to be carried 

forward to FY17.

 

1 This information is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best 

science. The information has not received final approval by the U.S. Geological Survey (USGS) and is provided on the 

condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized 

or unauthorized use of the information.
4

 FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 2: Streamflow, Water Quality, and Sediment Transport in the Colorado River Ecosystem

Program Manager 

(PM) David Topping Principal Investigator(s) (PI)

David Topping, USGS, GCMRC

Ronald Griffiths, USGS, GCMRC

David Dean, USGS, GCMRC

Email dtopping@usgs.gov

Telephone (928) 556-7396

SUMMARY

The Streamflow, Water Quality, and Sediment Transport Core Monitoring Project is focused on highresolution monitoring of stage, discharge, water temperature, specific conductance, dissolved oxygen, 

turbidity, suspended-sediment concentration, and particle size at 8 mainstem and 16 tributary sites located 

throughout the Colorado River Ecosystem (CRE). These data are collected to address GCDAMP GOAL 7 and 

are used to inform managers on the physical status of the Colorado River in the CRE and how this physical 

status is affected by dam operations in near real time. The high-resolution suspended-sediment data collected 

under this project are used to construct the mass-balance sediment budgets used by managers to trigger HFE 

under the 2012–2020 High-Flow Protocol. Details of this ongoing project (including descriptions of the datacollection locations) are provided in the GCMRC 2015–17 Triennial Work Plan.

Science Question Addressed:

The Streamflow, Water Quality, and Sediment Transport Core Monitoring Project addresses the following 

fundamental science question in an ongoing manner:

"How do operations at Glen Canyon Dam affect flows, water quality, sediment transport, and 

sediment resources in the CRE?"

During FY16, this question was addressed through:

1) Maintenance and continual updating of the database and website 

at http://www.gcmrc.gov/discharge_qw_sediment/ or http://cida.usgs.gov/gcmrc/discharge_qw_sedim

ent/. All stage, discharge, water quality (water temperature, specific conductance, turbidity, dissolved 

oxygen), suspended-sediment, and bed-sediment data collected at all active and inactive monitoring 

stations on the Colorado River and its tributaries are posted at this website. User-interactive tools at 

this website allow visualization and downloading of these data and the construction of sand budgets 

and duration curves (this is a new tool completed this year).

2) Publication of 3 peer-reviewed interpretive papers. The interpretive papers published during FY16 

focused on: a physically based method for using multi-frequency acoustics to measure suspendedsediment concentration and grain size in the Colorado and other rivers, and turbidity in the Colorado 

River.

Six additional peer-reviewed publications will be completed during the remaining period of the 2015-17 Work 

Plan, with perhaps the most important of these publications having the working title "Evaluation of the effects 

of 2008-2016 dam operations on sediment storage dynamics within the CRE."

Selected FY16 results:
5

During FY16, all monitoring data required by this project, including those required to trigger and design the 

Nov. 2016 HFE, were collected. Processing of all data is complete and all data have been uploaded to and are 

available at our website, except for laboratory analyses of some of the suspended-sediment data from 

automatic pump samplers (this task will be completed by the end of February 2017, as is the usual schedule 

for this project). The large amount of data collected and analyzed by this project makes it impossible to 

synthesize all results herein. Thus, all data and user-interactive tools for visualizing the data are available at 

our website, with a synthesis of only selected key parameters provided in Table 1. Years in which 

demonstrable change in sand mass (i.e., years in which sand was gained or lost) occurred in the selected 

reaches are indicated by bold type. 

Table 1. Status of selected key parameters in the CRE during the last 5 years

FY 2012 FY 2013 FY 2014 FY 2015 FY 2016

Median Colorado 

River (CR) discharge 

at Lees Ferry 

12,500 cfs 10,700 cfs 9,800 cfs 12,100 cfs 12,400 cfs

June-Oct Paria River 

sand input

690,000 metric 

tons

1,900,000 

metric tons

1,200,000 

metric tons

1,600,000 

metric tons

880,000 metric 

tons

Upper Marble 

Canyon sand budget 

+480,000 

±130,000 

metric tons

+1,400,000 

±320,000 

metric tons

+160,000 

±250,000 

metric tons

-130,000 

±240,000 

metric tons

+210,000 

±390,000 

metric tons

Lower Marble 

Canyon sand budget

+89,000 

±39,000 metric 

tons

+140,000 

±84,000 

metric tons

+500,000 

±120,000 

metric tons

+220,000 

±140,000 

metric tons

+130,000 

±130,000 

metric tons

Eastern Grand 

Canyon sand budget 

-29,000 

±90,000 metric 

tons

-110,000 

±190,000 

metric tons

-310,000 

±150,000 

metric tons

-850,000 

±230,000 

metric tons

-350,000 

±180,000 

metric tons

Water temperature 

exceeded 10% of the 

time in CR below the 

LCR (RM 66)

14.4o C 12.8o C 15.2o C 14.9o C 14.6o C

Turbidity exceeded 

10% of the time in CR 

above the 

LCR (RM 61) 

66 FNU 158 FNU 68 FNU 149 FNU 100 FNU

Median and max. CR 

specific conductance 

(a proxy for salinity) 

at Lees Ferry 

665 μS/cm 

at 25oC

805 μS/cm at 

25o

C

737 μS/cm at 

25oC

890 μS/cm at 

25o

C

832 μS/cm at 

25oC

960 μS/cm at 

25o

C

751 μS/cm at 

25oC

884 μS/cm at 

25o

C

737 μS/cm at 

25oC

867 μS/cm at 

25o

C

Median and min. CR 

dissolved oxygen at 

Lees Ferry 

8.2 mg/L

5.9 mg/L

7.9 mg/L

5.6 mg/L

7.5 mg/L

5.5 mg/L

7.9 mg/L

5.0 mg/L

7.7 mg/L

5.1 mg/L

In addition to the collection, processing, and web posting of all monitoring data, presentation of 5 papers at 

professional science meetings, and completion of 3 peer-reviewed publications, we completed and released on 

our website the duration-curve tool promised in the 2015–17 Triennial Work Plan. This new tool allows the 
6

user to plot (in linear or log space) the percentage of time that any continuously monitored parameter is 

equaled or exceeded during any user-selected time period. This new way of plotting data on our website is 

incredibly powerful and allows the user to (1) quickly visualize the amount of time any value of any 

parameter occurs, and (2) quickly determine of the maximum, minimum, and median (i.e., 50th-percentile) 

values of any parameter over any time period. To use this new tool, please: 

1) Go to any monitoring station.

2) Select a parameter to plot.

3) Input the time period to plot.

4) Click "Build Graph."

5) After time series plot appears in the window, click "Duration Curve Plot."

6) If the option is given, select a linear or logarithmic y-axis depending on your preference. Using the 

logarithmic y-axis yields a smoother duration curve at lower values of the plotted parameter.

7) Slider below plot can be used to zoom in to a smaller range for the x-axis.

8) Red ball and line can be dragged across the plot with mouse to see values along curve.

Below are a time-series plot (left) and a duration-curve plot (right) for water temperature during FY15 in the 

Colorado River near river mile 66 below the mouth of the Little Colorado River.

Suggestions and rationale for next steps:

It is recommended that this project continue in its current form because: (1) the stage, discharge water quality, 

and sediment data collected by this project in the CRE are the basic data used by every other project funded 

by the Glen Canyon Dam Adaptive Management Program, and (2) the data collected by this project are used 

to trigger, design, and evaluate HFEs under the 2012–2020 High-flow protocol and operations under the 

LTEMP EIS. 
7

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Online 

database 

and webbased 

applicatio

ns

Discharge, sediment 

transport, water-quality, 

and sand-budget data are 

served through the 

GCMRC website. A webbased application has been 

maintained to provide 

stakeholders, scientists, 

and the public with the 

ability to perform 

interactive online data 

visualization and analysis, 

including the on-demand 

construction of sand 

budgets and duration 

curves. These capabilities 

are unique in the world.

ongoing

updated 

every 

month

updated 

every 

month

http://www.gcmrc.gov/di

scharge_qw_sediment/

http://cida.usgs.gov/gcm

rc/discharge_qw_sedim

ent/

Online 

realtime 

database

Discharge and waterquality data collected at 9 

gaging stations by the 

Utah and Arizona Water 

Science Centers under 

project are posted to the 

web every hour.

n/a hourly n/a http://waterdata.usgs.go

v/nwis

Abstracts

presented 

at 

profession

al 

meetings

American Geophysical 

Union abstract for 2015 

Fall Meeting entitled 

"Flash Floods, Sediment 

Transport, and the 

Geomorphic 

Transformation of 

Moenkopi Wash, AZ."

Presentation made at AGU 

in December 2015.

FY16 Dec. 2015 Dec. 2015

Topping, D.J., and 

Dean, D.J., 2015, Flash 

Floods, Sediment 

Transport, and the 

Geomorphic 

Transformation of 

Moenkopi Wash, AZ:

Abstract H51E-1419 

presented at 2015 Fall 

Meeting, AGU, San 

Francisco, Calif., 14-18 

Dec.

American Geophysical 

Union abstract for 2015 

Fall Meeting entitled 

FY16 Dec. 2015 Dec. 2015

Grams. P.E., Buscombe, 

D., Hazel, J.E., 

Kaplinksi, M.A., and 
8

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

"Patterns of Channel and 

Sandbar Morphologic 

Response to Sediment 

Evacuation on the 

Colorado River in Marble 

Canyon, Arizona."

Presentation made at AGU 

in December 2015.

Topping, D.J., 2015, 

Patterns of Channel and 

Sandbar Morphologic 

Response to Sediment 

Evacuation on the 

Colorado River in 

Marble Canyon, 

Arizona: Abstract 

EP33A-1035 presented 

at 2015 Fall Meeting, 

AGU, San Francisco, 

Calif., 14-18 Dec.

American Geophysical 

Union abstract for 2015 

Fall Meeting entitled 

"Measurement of sediment 

loads during flash flood 

events: 14 years of results 

from a six stream 

monitoring network on the 

southern Colorado 

Plateau." Presentation 

made at AGU in December 

2015.

FY16 Dec. 2015 Dec. 2015

Griffiths, R.E., and 

Topping, D.J., 2015, 

Measurement of 

sediment loads during 

flash flood events: 14 

years of results from a 

six stream monitoring 

network on the southern 

Colorado Plateau:

Abstract H51E-1416 

presented at 2015 Fall 

Meeting, AGU, San 

Francisco, Calif., 14-18 

Dec.

American Geophysical 

Union abstract for 2015 

Fall Meeting entitled 

"Interpreting Hydraulic 

Conditions from 

Morphology, 

Sedimentology, and Grain 

Size of Sand Bars in the 

Colorado River in Grand 

Canyon." Presentation 

made at AGU in December 

2015.

FY16 Dec. 2015 Dec. 2015

Rubin, D.M., Topping, 

D.J., Schmidt, D.J., 

Grams, P.E., Buscombe, 

D., East, A.E., and 

Wright, S.A., 2015, 

Interpreting Hydraulic 

Conditions from 

Morphology, 

Sedimentology, and 

Grain Size of Sand Bars 

in the Colorado River in 

Grand Canyon:

INVITED Abstract 

EP41D-01 presented at 
9

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

2015 Fall Meeting, 

AGU, San Francisco, 

Calif., 14-18 Dec. 

Abstracts

presented 

at 

profession

al 

meetings 

(continued

)

International Association 

for Hydro-Environment 

Engineering and Research 

abstract for River Flow 

2016, Proceedings of the 

Eighth International 

Conference on Fluvial 

Hydraulics entitled "Longterm continuous acoustical 

suspended-sediment 

measurements in rivers –

Theory, evaluation, and 

results from 14 stations on 

five rivers." Presentation 

made in July 2016.

FY16 Jul. 2016 Jul. 2016

Topping, D.J., Wright, 

S.A., Griffiths, R.E., and 

Dean, D.J., 2016, Longterm continuous 

acoustical suspendedsediment measurements 

in rivers – Theory, 

evaluation, and results 

from 14 stations on five 

rivers, in 

Constantinescu, G., 

Garcia, M., and Hanes, 

D., eds., River Flow 

2016, Proceedings of the 

International 

Conference on Fluvial 

Hydraulics, St. Louis, 

Missouri, USA, July 11-

14, 2016, ISBN 978-1-

138-2913-2, p. 520-522.

Journal 

articles 

and other 

major 

pubs.

U.S. Geological Survey 

Professional Paper entitled 

"Long-term continuous 

acoustical suspendedsediment measurements in 

rivers—Theory, 

application, bias, and 

error."

FY16 May 2016 May 2016

Topping, D.J., and 

Wright, S.A., 2016, 

Long-term continuous 

acoustical suspendedsediment measurements 

in rivers—Theory, 

application, bias, and 

error: U.S. Geological 

Survey Professional 

Paper 1823, 98 

p., http://dx.doi.org/10.3

133/pp1823. 

International Association 

for Hydro-Environment 

Engineering and Research 

proceedings article for 

FY16 Jul. 2016 Jul. 2016

Topping, D.J., Wright, 

S.A., Griffiths, R.E., and 

Dean, D.J., 2016, Longterm continuous 
10

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

River Flow 2016, the 

Eighth International 

Conference on Fluvial 

Hydraulics entitled "Longterm continuous acoustical 

suspended-sediment 

measurements in rivers –

Theory, evaluation, and 

results from 14 stations on 

five rivers."

acoustical suspendedsediment measurements 

in rivers – Theory, 

evaluation, and results 

from 14 stations on five 

rivers, in 

Constantinescu, G., 

Garcia, M., and Hanes, 

D., eds., River Flow 

2016, CD-ROM 

Proceedings of the 

International 

Conference on Fluvial 

Hydraulics, St. Louis, 

Missouri, USA, July 11-

14, 2016, ISBN 978-1-

138-2913-2 for set of 

Book and CD-ROM, 

ISBN 978-1-315-64447-

9 for eBook PDF, p. 

1510-1518 on CDROM.

U.S. Geological Survey 

Fact Sheet entitled "Water 

clarity of the Colorado 

River—Implications for 

food webs and fish 

communities."

FY16 Nov. 2016 Sep. 2016

Voichick, N., Kennedy, 

T., Topping, D., 

Griffiths, R., and Fry, 

K., 2016, Water clarity 

of the Colorado River—

Implications for food 

webs and fish 

communities: U.S. 

Geological Survey Fact 

Sheet 2016-3053, 4 

p., http://dx.doi.org/10.3

133/fs20163053.
11

Project 2 Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $659,000 $5,000 $52,000 $0 $496,000 $85,798 $1,297,798

Actual

Spent $493,844 $9,738 $165,949 $0 $466,626 $80,230 $1,216,388

(Over)/Under

Budget $165,156 ($4,738) ($113,949) $0 $29,374 $5,568 $81,410 

FY15 

Carryover $44,657 CPI Decrease ($65,706) FY16 Carryover $60,361 

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Salary costs decreased due to charging to other reimbursable projects and vacancies.

- Operating expenses increased due to replacing broken instruments.

- Suballocations to other USGS cost centers increased due to sending additional funds to CIDA.

- Carryover will be used to send funds to CIDA, to replace old instruments and to offset FY17 shortage.
12

FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 3: Sandbars and Sediment Storage Dynamics: Long-term Monitoring and Research at the Site, 

Reach, and Ecosystem Scales

Program Manager 

(PM) Paul Grams Principal Investigator(s) (PI)

Paul Grams, USGS, GCMRC

Daniel Buscombe, USGS, 

GCMRC

Erich Mueller, USGS, GCMRC

Keith Kohl, USGS, GCMRC

Joel Sankey, USGS, GCMRC

Joseph Wheaton, Utah State Univ.

Brandon McElroy, Univ. Of 

Wyoming

Mark Schmeeckle, Arizona State 

Univ.

Joe Hazel, Northern Arizona 

Univ.

Matt Kaplinski, Northern Arizona 

Univ.

Email pgrams@usgs.gov

Telephone (928) 556-7385

SUMMARY

Sandbar Monitoring and Research (elements 3.1.1, 3.1.2, 3.1.3, 3.1.4, and 3.3)

The overall objectives of the sandbar monitoring and research project elements in the FY15–-17 work plan 

are to track sandbar and campsite size and abundance as they are affected by individual High-Flow 

Experiments (HFEs, or “controlled floods”) and successive HFEs and intervening dam operations. These 

projects are designed to evaluate whether the HFE protocol is having the intended effect of increasing sandbar 

size and abundance. Research elements of this project are designed to advance general understanding of eddy 

sandbar dynamics to improve capacity to predict the effects of dam operations on sandbars.

Annual changes in sandbars and campsites were measured by repeat topographic surveys at 47 long-term 

monitoring sites in September/October 2015 and September/October 2016. Remote cameras installed at 43 of 

these sites record daily changes in sandbar size. The 

repeat topographic surveys show that, in October 

2015, approximately 11 months after the 2014 HFE 

(the 3rd HFE released as part of the HFE protocol), 

the total volume of sand within sandbar monitoring 

sites was greater than before the start of the protocol 

in Marble Canyon and Grand Canyon (Figure 1). The 

surveys demonstrate that the HFE protocol was 

resulting in net deposition and the erosional trend that 

occurred in the 1990s and early 2000s is no longer 

occurring. Data from the 2016 monitoring trip are 

currently being processed and will be available at the 

January 2017 Annual Reporting meeting.
13

Figure 1. Average normalized sand volume for 19 long-term sandbar monitoring sites in Marble Canyon (River Mile 0 to 62) and 20 sites in Grand 

Canyon (River Mile 62 to 225). Each point is the average is for all monitoring sites in each segment with error bars showing standard error. The 

normalization is the ratio of the volume measured at a given date to the maximum observed for the entire monitoring record.

Only partial results from the November 2016 HFE are available at this time. Preliminary inspection of images 

from 14 remote camera sites between Phantom Ranch and Diamond Creek (River Mile 225) show substantial 

net deposition at 9 sites (Figure 2) and erosion or no net change at 5 sites. Images from the remaining 29 

remote cameras will be collected on the next GCMRC river trip in late January.

 

Figure 2. Photographs showing sandbar deposition that occurred during the November 2016 HFE at sandbar on river right approximately 119 miles 

downstream from Lees Ferry. The pre-HFE photo (left) was taken on November 7, 2016 and the post-HFE photo (right) was taken on November 13.

During FY16, significant progress has also been made in research-oriented projects, which include 

developing methods for automated analysis of the remote camera images, evaluation of structure-from-motion 

(SfM) methods for measuring sandbar topography, geochemical composition of HFE sand deposits, and 

sandbar modeling. A preliminary method for automated measurement of sandbar area from remote camera 

images has been developed and is being applied at selected sites. We anticipate presenting results showing 

weekly or monthly changes in sandbar area for selected sites by the end of FY17.

The SfM photogrammetry method allows “surveying” sandbar topography with ordinary digital cameras. We 

have developed an operational method for collection of images using a camera mounted on a 5-m pole and are 

in the process of evaluating errors in the method when compared to conventional topographic surveys. 

Preliminary results indicate the method provides high-resolution data over the unvegetated portions of the 

sandbars with a level of effort similar to that required for a conventional survey. Collection of images from an 

aerial platform (such as an unmanned aerial vehicle) would likely make the method more efficient [14].

We have analyzed the geochemical composition of HFE sand deposits using X-ray fluorescence in an effort to 

independently estimate the source of the sand contained in the deposits. Preliminary results indicate that sand 

derived from the Paria River can be distinguished geochemically from sand found in old pre-dam deposits. 

Results from a multi-variate mixing model suggest that recent HFE deposits consist of approximately 50% 

recent Paria River sand and 50% other sand, which may include old pre-dam sand and sand from other 

tributaries [6, 7, 8].

The goal of the sandbar modeling project element is to improve our understanding of the factors that 

contribute to spatial variability in sandbar response to HFEs and other flows and use this information to 

improve the sandbar monitoring design and better predict sandbar response to dam operations. In FY16, we 

delineated groupings of sandbar sites using a statistical analysis based on sandbar response metrics, 

geomorphic metrics, and vegetation abundance. This analysis connects sandbar behavior with easily measured 

site characteristics and will be used to predict response at sites not currently included in the set of long-term 

monitoring sites. The grouping distinguishes sites that tend to have less vegetation and substantial deposition 

caused by HFEs from sites that have more vegetation and less HFE deposition. Preliminary results from 
14

numerical flow modeling at these sites suggests that vegetation encroachment decreases flow strength in parts 

of the eddy, which may impede sand transport and sediment deposition [1, 11, 12, 13].

Sand Storage Monitoring and Research (elements 3.2, 3.4, and 3.5)

The goal of the sediment storage project is to track trends in the quantity of sand stored in the channel and in 

eddies over the time scale of long-term management actions, such as the HFE protocol. An additional purpose 

of this project is to track the location of changes in sand storage between the channel and eddies and between 

high- and low-elevation deposits. This monitoring involves repeat measurements of the river bed and banks 

over long reaches and studies to improve methods for measuring sand storage, bed composition, and sand 

transport.

The specific goals for the first two years of the FY15–17 work plan were to map the river channel in Glen 

Canyon (FY15) and map the river channel in upper Marble Canyon (FY16). The entire river channel between 

Glen Canyon Dam and Lees Ferry was mapped and the data have all been processed. These data have been 

used for flow modeling to support Project 5 and evaluation of the “Hidden Slough” site where green sunfish 

were found in 2015. Final maps for this reach and analysis that compares the 2015 measurements to previous 

measurements made in 2000 will be completed in FY17. In May 2016, we mapped the river bed and banks in 

Upper Marble Canyon (River Mile 0 to 32). These data are currently being processed and we expect to have 

preliminary results and comparisons with measurements made in 2013 by the end of FY17. In support of 

mapping efforts, we have expanded and evaluated the accuracy of the geodetic control network. Local 

accuracy is within 3.4 cm at the 95% confidence level, which provides the ability to integrate studies and 

support sandbar and sand storage monitoring.

In addition to mapping the river bed in Upper Marble Canyon, we evaluated methods for measuring bed-sand 

thickness using low-frequency “chirp” sonar. With the instrument we evaluated, we were able to estimate 

sand thickness in locations where there was approximately 2 m of sand or less. These data represent a 

significant first step in the effort to develop an absolute estimate of sand storage. In 2017, we will evaluate the 

feasibility of using more powerful instruments that might penetrate greater sand thicknesses. However, these 

instruments are designed for deployment in deep marine environments and may be difficult to use 

successfully in the Colorado River. 

Progress was also made on two additional research components of Project 3. For the bedload transport project 

(Project 3.4), we collected measurements of bedload transport during the November 2016 HFE on the 

Colorado River near Diamond Creek. These data, along with data collected in 2015, are being used to develop 

a new bedload transport model that will predict bedload as a function of streamflow and sediment parameters 

that are routinely measured at sediment monitoring stations. This information is expected to reduce the 

uncertainty in estimates of sand loads made in Project 2. For the bed classification project component (joint 

with Project 10), we have continued to advance methods for processing high-resolution bathymetric data [4, 

5] and we have developed methods to classify bed sediment composition from low-cost sidescan sonar 

images [3,10]. These methods will be used to develop bed-sediment composition maps that correspond with 

fish sampling efforts in April 2014 and April 2015. These data will be used to evaluate changes in reachaverage habitat conditions over the duration of native and non-native fish sampling projects.

Publications and Presentations:

1. Alvarez, L., Schmeeckle, M., Grams, P.E., accepted pending revision, A Detached Eddy Simulation 

Model for the Study of Lateral Separation Zones along a Large Canyon-Bound River, J. Geophys. 

Res. Earth Surf., 121, doi:10.1002/2016JF003895.
15

2. Ashley, T., McElroy, B., Buscombe, D., Grams, P., and Kaplinski, M., 2016, Estimating bedload 

from gage data to improve flux-based sediment budgets, Presentation at Geological Society of 

America Fall Meeting, Denver, CO.

3. Buscombe, D., in review, PyHum: Python toolbox for shallow water physical habitat assessment 

using recreational grade sidescan sonar. Environmental Modeling and Software

4. Buscombe, D., 2016, Spatially explicit spectral analysis of point clouds and geospatial data. 

Computers and Geosciences 86, 92-108, 

10.1016/j.cageo.2015.10.004. http://www.sciencedirect.com/science/article/pii/S0098300415300704

5. Buscombe, D., and Grams, P.E., 2016. Stochasticity of riverbed backscattering, with implications for 

acoustical classification of non-cohesive sediment using multibeam sonar. Proceedings of the 8th 

International Conference on Fluvial Hydraulics, St. Louis, Missouri, July 2016.

6. Chapman, K., Parnell, R. A., Smith, M. E., Grams, P. E., Mueller, E. R., 2015, Use of composite 

fingerprinting technique to determine contribution of Paria River sediments to dam-release flood 

deposits in Marble Canyon, Grand Canyon, AZ: Abstract EP23E-03 presented at 2015 Fall Meeting, 

AGU, San Francisco, California, 14-18 December. 

7. Chapman, K., 2016, Quantifying tributary-supplied sediment contribution to experimental flood 

deposits in Marble Canyon, AZ, presented at 2016 Hydro Research Fellow Roundtable Meeting, 

HydroVision International, Minneapolis, Minnesota, 26-29 July. 

8. Chapman, K., Parnell, R. A., Smith, M. E., Grams, P. E., Mueller, E. R., 2016, Evaluating the 

effectiveness and long-term sustainability of experimental floods on the Colorado River in the Marble 

Canyon reach of Grand Canyon, AZ, presented at the 2016 Fall Meeting, GSA, Denver, Colorado, 

25-28 September.

9. Grams, P. E., J. C. Schmidt, S. A. Wright, D. J. Topping, T. S. Melis, and D. M. Rubin (2015), 

Building Sandbars in the Grand Canyon, EOS, Trans. Am. Geophys. Union, 96(11), 12–

16. https://eos.org/features/building-sandbars-in-the-grand-canyon

10. Hamill, D., Buscombe, D., et al., 2016, Towards bed texture change detection in large rivers from 

repeat imaging using recreational grade sidescan sonar. Proceedings of the 8th International 

Conference on Fluvial Hydraulics, St. Louis, Missouri, July 2016.

11. Mueller, E.R., Grams, P.E., Hazel, Jr., J.E., and Schmidt, J.C., 2016, Variability of eddy sandbar 

response during two decades of controlled flooding along the Colorado River in Grand Canyon. 

Geological Society of America Annual Meeting, Denver, CO. Sept. 2016.

12. Mueller, E.R., Grams, P.E., Topping, D.J., Schmidt, J.C., Wright, S.A., Melis, T.S., Rubin, D.M., 

Hazel, Jr., J.E., and Kaplinski, M., 2016, Science-based strategies for experimental flooding in Grand 

Canyon. National Conference on Ecological Restoration, Coral Springs, FL. Apr. 2016.

13. Mueller, E.R., Grams, P.E., Hazel, J.E. Jr., and Schmidt, J.C. (in preparation) Linkages between eddy 

sandbar dynamics and riparian vegetation during two decades of controlled flooding along the 

Colorado River in Grand Canyon. *Invited manuscript for Sedimentary Geology*

14. Rossi, R., Buscombe, D., Grams, P., and Wheaton, J., 2016, From Hype to an Operational Tool: 

Efforts to Establish a Long-Term Monitoring Protocol of Alluvial Sandbars using ‘Structure-fromMotion’ Photogrammetry, Presentation at 2016 Fall Meeting, AGU, San Francisco, CA.
16

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

data

Project 3.1.1: Data from 

long-term sandbar 

monitoring sites Annual Jan. 2016; 2017 --

To be presented at annual 

reporting meeting 

and www.gcmrc.gov/sand

bar

photos

Project 3.1.1: Images from 

remote camera monitoring 

of sandbars

Annual Jan. 2016; 

2017 -- Website: www.gcmrc.gov/sandbar

article

Project 3.1.1: New High 

Flow Protocol Contributes 

to Sandbar Gains in Grand 

Canyon

FY16 Jun. 2015 -- Publication: [9]

map/re

port

Project 3.1.2: Geomorphic 

base map and map of high 

elevation sand from 2013 

images

FY16 Apr. 2017 Mapping in progress, 

report in preparation

Project 3.1.3 and 3.1.4: No 

FY16 products. Presentations: [14]

report

Project 3.2: Report on 

acoustic detection of 

submerged aquatic 

vegetation

FY16 2016 Aug. 2017

Publication [3]; 

Presentations [5, 10]; 

additional publication 

expected in 2017

report

Project 3.2: Spatially 

explicit spectral analysis 

of point clouds

FY16 2016 Publication [4]

report

Project 3.2: Report and 

maps on sand storage 

change in Glen Canyon

FY16 Jun. 2017

Data processing complete 

maps and report in 

progress.

article Project 3.3: Article on 

flow modeling FY16 2016 Publication [1]

report

Project 3.3: Article on 

generalized sandbar 

groupings.

FY16 Jan. 2017 Article [13]; Presentations 

[11;12]

Project 3.4: No FY16 

products.

Presentation [2]
17

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

report

Project 3.5: Report on 

geodetic control including 

GPS observations and 

leveling data.

FY16 Feb. 2017 Report in review.

Project 3 Salaries Travel & 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $581,400 $5,900 $46,000 $448,900 $20,000 $89,355 $1,191,555

Actual

Spent $462,856 $16,735 $136,892 $505,898 $27,379 $89,050 $1,238,810

(Over)/Under

Budget $118,544 ($10,835) ($90,892) ($56,998) ($7,379) $305 ($47,255)

FY15 

Carryover $81,793 CPI Decrease ($60,327) FY16 Carryover ($25,789)

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Salary costs decreased due to receiving non-AMP funds.

- Operating Expenses increased due to Purchase of new sonar and navigation system for river bed mapping 

(shared purchase between AMP, non-AMP & USGS funds). Construction of new underwater camera system for 

bed surface grain size cost more than planned.

- Cooperative Agreement Expenses increased due to increased involvement by cooperators.

- Shortfall will be made up in FY17.
18

FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 4: Connectivity Along the Fluvial-Aeolian-Hillslope Continuum: Quantifying the Relative 

Important of River-Related Factors that Influence Upland Geomorphology and Archaeological Site 

Stability

Program Manager 

(PM) Joel Sankey Principal Investigator(s) (PI)

Joel Sankey, USGS, GCMRC

Amy East, USGS, PCMSC

Helen Fairley, USGS, GCMRC

Josh Caster, USGS, GCMRC

Alan Kasprak, USGS, GCMRC

Email jsankey@usgs.gov

Telephone (928) 556-7289

SUMMARY

Project 4. Overview

Dam-released flows affect the deposition and retention of sand bars that serve as sources for other sand 

resources throughout the Colorado River ecosystem. Wind transport of sand from sandbars located near the 

active river channel to higher elevation valley margins can, in turn, affect the geomorphic condition of 

archaeological sites and the characteristics of other cultural and natural resources in the ecosystem. The 

degree to which valley margins are affected by upslope wind redistribution of river-derived sand is called 

sediment “connectivity” (Figure 1). Connectivity is affected by several factors including the amount of sand 

supplied as well as physical and vegetative barriers to sand transport. The primary hypothesis of this project is 

that high degrees of connectivity lead to greater archaeological site stability and increase the potential for 

preservation in place of buried archaeological features via aeolian sand deposition and/or mitigation of gully 

erosion. 

Figure 1. Conceptual overview of geomorphic processes that are important for sediment connectivity

This project is composed of two integrated elements: the first (4.1) is a research element, and the second (4.2) 

is a monitoring element. The research element (4.1) consists of two sub-elements; both of these are landscape 

scale analyses that examine the connectivity between attributes of the active channel and geomorphic 

processes and patterns at higher elevations (above the 45,000 ft3

/s stage) at several spatiotemporal scales. In 

the monitoring element (4.2), all of FY15 was invested to develop and draft a long-term plan to monitor the 
19

geomorphic condition of archaeological sites in the Colorado River corridor. The monitoring plan was then 

implemented in FY16 and will be continued in FY17 through the triennial work plan (TWP).

The project elements and sub-elements are:

(4.1) Quantifying connectivity along the fluvial-aeolian-hillslope continuum at landscape scales

(4.1.1) Examine landscape-scale spatial variability using a combination of remote sensing and 

GIS analyses

(4.1.2) Conduct visual interpretation of historical oblique photos to assess whether hypothesized 

changes due to dam operations are supported by photographic evidence.

(4.2) Monitoring of cultural sites in Grand and Glen Canyons

Please note that there was a third sub-element (4.1.3) in Project 4 of the TWP which was not funded and 

therefore not pursued by GCMRC staff during the implementation of the TWP.

Project Element 4.1. Connectivity along the fluvial-aeolian-hillslope continuum

Project element 4.1 proposes to quantify relationships between the distribution of sand within the active river 

channel and the distribution of higher elevation river-derived (“aeolian”) sand to identify what environmental 

factors related to dam operations control the location and size of aeolian sand deposits that are found above 

the maximum controlled flood stage.

Sub-element 4.1.1 

In FY16 we published a seminal USGS Professional Paper entitled “Conditions and Processes Affecting Sand 

Resources at Archaeological Sites in the Colorado River Corridor Below Glen Canyon Dam, Arizona” which 

is based on work completed during Project 4 of the TWP, Project J of the 2013/14 Biennial Work Plan 

(BWP), and by other related projects during the previous ~10 years.

Key findings presented in the professional paper are that under current dam operations elevated baseflows and 

infrequent HFEs without large sediment-rich floods (i.e., greater than 45,000 ft3/s) promote the expansion of 

riparian vegetation onto bare sand and limit the duration of time that sand is subaerially exposed and therefore 

available for aeolian transport. This in turn results in landscapes above the stage of HFEs that contain less 

active aeolian sand and are therefore more erodible by rainfall runoff than they could be if the dam were 

operated differently. We determined from lidar topographic surveys that most sites lost sand from erosion 

during 2006–2014 and that sand loss from erosion exceeded aeolian deposition of river-derived sand for these 

sites. Nonetheless, we also determined that many archaeological sites exist in source-bordering aeolian 

dunefields that are clearly coupled with upwind river sand supplies (sandbars) and it is also clear that riversourced sand deposition at such sites is a time-dependent process and the outer limit of that process may 

extend for many years after any individual HFE. 

Since the implementation of the current HFE protocol, HFEs have occurred at a relatively high frequency 

(i.e., once annually in 2012, 2013, 2014, and 2016). The question of how higher frequency HFEs will affect 

sediment connectivity and geomorphic condition at archaeological sites that are geomorphically coupled to 

the active river channel is currently unanswered (e.g., was not answered in the professional paper) but is very 

important for understanding the impacts of the HFE protocol on sandy landscapes above the 45,000 ft3

/s 

stage. Thus during FY15 and FY16 we initiated a study of new and archived data to understand the impact of 

HFEs on aeolian landscapes within the context of our focus on connectivity. In particular, the findings of the 

professional paper together with this new work suggest that the current protocol of near-annual HFEs in 

conjunction with targeted vegetation removal could eventually lead to net sediment deposition at some 
20

archaeological sites and source-bordering dunefields and thereby increase the potential for preservation in 

place of buried archaeological features at these locations. 

The wealth of topographic data collected during the FY15–17 TWP, FY13–14 BWP, and previous research 

and monitoring efforts along the Colorado River over the past ~10 years make it possible for us to examine, 

for the first time, the effect of contrasting dam operation regimes (i.e., hydrographs) on the geomorphic 

response or sediment budget of selected sand resources and archaeological sites. In this regard, we focused on 

two avenues of research in FY15 and 16. Our first task was to develop a robust, reproducible, and automated 

approach for analyzing these large volumes of archived topographic data in the form of original software. 

These novel tools are in the process of being published in peer-reviewed literature, but are already being used 

in Project 4 research and monitoring to determine the changes in geomorphic condition at archeological sites 

during the current HFE protocol. 

Our second research effort focuses on analyses of the individual and coupled roles of (a) flow regime and (b) 

vegetation encroachment on the amount of sand exposed (i.e., available) for aeolian transport and 

preservation of archaeological sites. The analyses integrate data from topographic surveys, vegetation 

mapping, and aeolian sediment mapping, along with bathymetric and aerial image-based sand mapping from 

Project 3 of the TWP for a 30-mile reach of the Colorado River in Lower Marble Canyon. Preliminary 

findings from this research indicate that hydrologic alteration by Glen Canyon Dam has reduced the areal 

extent of sand available for aeolian transport by 14% compared with the pre-dam period, with an additional 

20% reduction in sand area resulting from vegetation encroachment onto surfaces previously covered by bare 

sand that has occurred since completion of Glen Canyon Dam through present day. One important reason for 

conducting these analyses is to inform where and how targeted vegetation removal might be useful for 

increasing sediment connectivity between the active river channel and other landscapes in the canyon.

Sub-element 4.1.2 

In sub-element 4.1.2., we are analyzing historical oblique photographs to ascertain the degree to which 

environmental conditions at or near cultural sites have changed during the past > 50 years by comparing 

conditions in areas that appear to have functioned as aeolian landscapes in the past to current conditions. 

Analyses focus on whether the historical photos shows more or less open sand bars, cryptobiotic crust cover, 

and vegetation cover within areas that appear to have served as sources of aeolian sand to cultural sites and 

landscapes with concentrations of cultural sites (Figure 2). The current state of cultural sites and aeolian 

landscapes are being similarly assessed based on more recent site photos as well as recent site descriptions 

(e.g., from site investigation work completed in 2013 and 2014). One anticipated outcome of this analysis will 

be an estimate of the proportion of cultural sites for which the potential influence of aeolian sand inputs has 

changed from pre-dam to recent post-dam time, relative to changes in environmental characteristics including 

vegetation and biologic crusts.
21

Figure 2. View of boat beach near Phantom Ranch. Top photo by E.C. LaRue in August 26th 1923, bottom by A.H. Fairley May 5th 2016. Red arrow 

points towards Bright Angel ruin which was partially buried by aeolian sand and excavated in 1969. Note growth of riparian vegetation which currently 

restricts sand transport from beach to ruin.

In FY16, we continued to locate and assess the suitability of existing historical photo collections for this analysis 

effort and on analyzing photographs from the Stanton photographic collection and matches of the Stanton 

photographs obtained by Dr. Robert Webb and colleagues in 1990–1992 and in 2010–2011. We also obtained 

digital copies of the 1923 USGS Birdseye expedition. During the May 2016 monitoring river trip, we took high 

resolution digital matches of approximately 40 of the 1,923 images. By the end of September, 2016, 

approximately 35% of the Stanton collection had been analyzed. While this is still a work in progress, the 

analysis completed to date confirms that aeolian source areas along the Colorado River have diminished 

significantly during the past 120 years due to two principal factors: 1) reduction in the size (volume) and 

abundance (number and extent) of river-deposited sand bars, and 2) increases in riparian vegetation below the 

old high water line. With regard to the second factor, the photographic analysis demonstrates that the amount 

of vegetation cover in the formerly active river channel below the mesquite line not only increased between 

1889–1890 and the early 1990s, but that it has continued to increase dramatically since 1990–1992 as a result 

of dam operations.

Project Element 4.2. Monitoring plan development and implementation 

The primary objective for Project Element 4.2 in FY15 and FY16 was to draft and subsequently implement a 

monitoring plan in response to stakeholders’ request for “establishing a long-term, systematic strategy for 

assessing the effects of dam operations on archaeological sites due to flow and non-flow actions.” The 

purpose of the document (see Monitoring Plan product below) was to provide a means for collecting 

information useful in Reclamation’s effort to maintain National Historic Preservation Act (NHPA) 

compliance under the Long Term Experimental and Management Plan (LTEMP). The proposed monitoring 

plan is designed to address specific target points outlined by BOR and NPS that were summarized in the 
22

Project 4 proposal of the TWP (M. Barger, email communication, May 19 2014, to J. Sankey; J. Balsom, 

email communication, July 7, 2014, to J. Schmidt, H. Fairley, G. Knowles). As NPS archaeologists and tribal 

representatives monitor cultural resource site integrity, the plan focuses on strategies for quantitative 

assessment of effects of geomorphic processes associated with dam operation on archaeological site 

condition. One important focus of the plan is to monitor whether, and to what degree, HFE sand is transported 

by wind to a representative sample of archaeological sites and to also quantify the effect of this windtransported sand on surface stability.

In May 2016 we completed the first monitoring trip under this plan during which we conducted lidar 

topographic surveys of 7 archaeological sites in source-bordering dunefields along the Colorado River in 

Grand Canyon and completed drainage classifications at more than 100 sites. We have completed the 

processing and summary of geomorphic change at all of the lidar survey sites by using the new software that 

we developed as part of project element 4.1 (see products by Kasprak et al., in review, journal manuscript, 

software, and data). We are now completing the analysis of these data with a post-hoc analysis of previous 

surveys acquired during the period of the contemporary HFE protocol (i.e., spanning the 2012, 2013, and 

2014 HFEs) using the same software to ensure reproducibility of our analyses. Results indicate that all of the 

sites with upwind HFE sandbar sources and with data spanning the HFE protocol time period, experienced 

some influx of windblown sand from HFE sandbars and that approximately half of the sites were net 

depositional,. 

We will complete another monitoring trip in May 2017 during which we propose to revisit most of the sites 

surveyed in 2016 and also survey several new sites as well. We will also complete drainage classifications for 

the remaining sites that have yet to be classified and then report on those monitoring data. Continuing this 

monitoring into the future and also analyzing the new data with the existing time series of surveys for several 

of the sites will allow us to continue to report on whether, and to what degree, HFE sand is transported by 

wind to a sample of archaeological sites and what effect wind-transported sand has on surface stability.

In addition, Project Element 4.2 entailed the continued operation of weather stations at six sites throughout 

Glen, Marble and Grand Canyons:

• Weather data were collected at six stations, one at Ferry Swale in Glen Canyon and one at Lees Ferry 

and one each at the four Marble-Grand Canyon archaeological sites AZ C:05:0031, C:13:0321, 

B:10:0225, and G:03:0072. Stations collected measurements at 4-minute resolution of rainfall, wind 

speed and direction, temperature, barometric pressure, and relative humidity. 

• At sites C:05:0031, C:13:0321, and B:10:0225, stationary cameras took photographs once per day to 

record qualitative information about the timing and nature of landscape change.

In February, the Project 4 team also worked in Glen Canyon with GLCA Archaeology staff to visit and 

classify all river corridor archeological sites using both the aeolian and drainage classification systems. A 

confidential report was drafted by the Project 4 team and is currently in review with GLCA archaeology staff. 

The purpose of the classification and report is to provide resource managers with a technical summary and 

review of modern landscape processes affecting each river corridor cultural site in the Glen Canyon National 

Recreation Area downstream of Glen Canyon Dam. A similar report was completed for river corridor sites in 

Grand Canyon National Park during the 2013–14 BWP.
23

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Journal 

Paper

Beyond Compliance: 

Designing a Monitoring 

Program to Document 

Downstream Dam Effects 

at Archaeological Sites in 

Glen and Grand Canyons, 

Arizona.

Spring 

2017

To be submitted in 

December to Advances in 

Archaeological Practice 

journal

Authors are: Fairley, 

Sankey, East, Collins, 

Caster, Kasprak

Journal 

Paper

Geomorphic Process from 

Topographic Form: 

Automating the 

Interpretation of Repeat 

Survey Data in River 

Valleys

Spring 

2017

Currently in review at 

Earth Surface Processes 

and Landforms journal

Authors are: Kasprak, 

Caster, Bangen, Sankey

Dataset and 

Software

“Software and Example 

Datasets for the Automated 

Classification of 

Geomorphic Processes in 

Repeat Topographic Survey 

Data”

Spring 

2017

Currently in review with 

USGS.

Authors are: Kasprak, 

Caster, Bangen, Sankey

Confidential 

Interagency 

Technical 

Report

Modern landscape 

processes affecting cultural 

sites in the Colorado River 

corridor below Glen 

Canyon Dam, Glen Canyon 

National Recreation Area, 

Arizona

Spring 

2017

Currently in review with 

Glen Canyon National 

Recreation Area

Archaeology Staff

Authors are: East, Sankey, 

Fairley, Caster, Kasprak

USGS 

Professional 

Paper

Conditions and processes 

affecting sand resources at 

archeological sites in the 

Colorado River corridor 

below Glen Canyon Dam, 

Arizona: U.S. Geological 

Survey Professional Paper 

1825

May 2016

East, A.E., Collins, B.D., 

Sankey, J.B., Corbett, 

S.C., Fairley, H.C., and 

Caster, J., 2016, 

Conditions and processes 

affecting sand resources at 

archeological sites in the 

Colorado River corridor 

below Glen Canyon Dam, 

Arizona: U.S. Geological 

Survey Professional Paper 

1825, 104 p., 

http://dx.doi.org/10.3133/

pp1825.
24

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Journal 

Paper

Relations between rainfall–

runoff-induced erosion and 

aeolian deposition at 

archaeological sites in a 

semi-arid dam-controlled 

river corridor

May 2016

Collins, B.D., Bedford, 

D.R., Corbett, S.C., 

Cronkite-Ratcliff, C., and 

Fairley, H.C. (2016) 

Relations between 

rainfall–runoff-induced 

erosion and aeolian 

deposition at 

archaeological sites in a 

semi-arid dam-controlled 

river corridor. Earth Surf. 

Process. Landforms, 

41(7): 899–917. doi: 

10.1002/esp.3874.

Monitoring 

Plan

Draft plan for monitoring 

effects of geomorphic 

processes at archaeological 

sites in Grand & Glen 

Canyon

Jan. 2016

Draft provided to 

stakeholders in 

Fall/Winter, 2016

Authors are: Sankey, 

Fairley, Caster, East

USGS 

Scientific 

Investigatio

ns Report

Variability in Rainfall at 

Monitoring Stations and 

Derivation of a Long-Term 

Rainfall Intensity Record in 

the Grand Canyon Region, 

Arizona, USA: U.S. 

Geological Survey 

Scientific Investigations 

Report 2016-5012

Feb 2016

Caster, J., Sankey, J.B., 

2016. Variability in 

Rainfall at Monitoring 

Stations and Derivation of 

a Long-Term Rainfall 

Intensity Record in the 

Grand Canyon Region, 

Arizona, USA: U.S. 

Geological Survey 

Scientific Investigations 

Report 2016-5012, 40 p., 

https://pubs.er.usgs.gov/pu

blication/sir20165012
25

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

USGS Open 

File Report 

and Dataset

Meteorological data for 

selected sites along the 

Colorado River Corridor, 

Arizona, 2011–13: U.S. 

Geological Survey OpenFile Report 2014-1247

Spring 

2017

New data is appended 

every other year to this 

report:

Caster, J., Dealy, T., 

Andrews, T, Fairley, H., 

Draut, A., Sankey, J., and 

Bedford, D., 2014, 

Meteorological data for 

selected sites along the 

Colorado River Corridor, 

Arizona, 2011–13: U.S. 

Geological Survey OpenFile Report 2014-1247, 56 

p., 

http://dx.doi.org/10.3133/

ofr20141247

Conference 

Presentation

Fairley, H.C., Sankey, J.B. 

and Caster, J., Designing a 

monitoring program to 

inform adaptive 

management of cultural 

resources in the context of a 

changing climate: an 

example from Glen and 

Grand Canyons, Arizona. 

Presented at Colorado 

Plateau Biennial 

Conference, Flagstaff, AZ.

Oct

2015

Conference 

Presentation

Caster, J., Kasprak, A., and 

Sankey J. B., But what does 

it mean? Geomorphic 

process attribution in 

DEMs-of-Difference 

derived from repeat lidar. 

Presented at USGS Lidar 

Science Innovation 

Workshop, Fort Collins, 

Co.

Aug 2016
26

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Conference 

Presentation

Kasprak, A., Caster, J., 

Bangen S., and Sankey 

J.B., 2016, So much data, 

so little time: automating 

the interpretation of repeat 

topographic survey data in 

river valleys, Presented at 

U.S. Geological Survey 

Postdoctoral and New 

Scientists Colloquium, 

Menlo Park, CA.

Sept 2016

Conference 

Presentation

Fairley, H.C., Sankey, J.B. 

East, A.E., and Caster, 

J.M., Sustaining sites in a 

sediment-deprived system:

designing a monitoring 

program to assess Glen 

Canyon dam effects on 

downstream archaeological 

sites in Grand Canyon, 

Arizona. Presented at 

Geological Society of 

America, September, 2016, 

Denver. CO.

Sept

2016

Conference 

Presentation

Caster, J., Kasprak, A., and 

Sankey J. B., Automating 

the mapping and 

measurement of 

geomorphic response to 

regulated river flows: A 

case study in Grand 

Canyon, AZ, Presented at 

the Geological Society of 

America annual conference, 

Denver, Co.

Oct

2016
27

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Conference 

Presentation

Kasprak A., Buscombe D, 

Caster J., Grams P.E., and 

Sankey, J.B., 2016, The 

individual and additive 

effects of vegetation 

encroachment and 

hydrologic alteration on 

sediment connectivity in 

Grand Canyon, Presented at 

2016 AGU Fall Meeting, 

San Francisco, CA.

Dec

2016

Conference 

Presentation

Sankey J., Kasprak A., 

Caster J., and Bangen S., 

2016. Geomorphic Process 

from Topographic Form: 

Automating the

Interpretation of Repeat 

Survey Data to Understand 

Sediment Connectivity for 

Source-Bordering Aeolian 

Dunefields in River 

Valleys. Presented at 2016 

AGU Fall Meeting, San 

Francisco, CA.

Dec 2016

Webex 

Presentation 

to Brief the 

Assistant 

Secretary 

for Water 

and Science

East, Collins, Sankey, 

Corbett, Fairley, Caster, 

Conditions and processes 

affecting sand resources at 

archaeological sites in the 

Colorado River Corridor. 

May, 2016.

May 2016

Webex 

Presentation 

to the 

Cultural 

Resources 

Stakeholder

s of the 

GCDAMP

East, Collins, Sankey, 

Corbett, Fairley, Caster, 

Conditions and processes 

affecting sand resources at 

archaeological sites in the 

Colorado River Corridor. 

May, 2016.

May 2016
28

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Webex 

Presentation 

to the TWG

East, Collins, Sankey, 

Corbett, Fairley, Caster, 

Conditions and processes 

affecting sand resources at 

archaeological sites in the 

Colorado River Corridor. 

May, 2016.

June 2016

Presentation 

at the 2016 

Annual 

Reporting 

Meeting

Caster, J, Sankey, J.B., 

East, A., Fairley, H., and 

Kasprak, A., Refining our 

understanding of sand 

distribution along the 

fluvial-aeolian-hillslope 

continuum: Preliminary 

results of Project 4 FY2015 

GIS analysis, GCDAMP 

annual reporting meeting, 

Phoenix, AZ

Jan 2016

Project 4 Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $285,000 $14,000 $63,000 $0 $87,300 $43,378 $492,678 

Actual

Spent $248,585 $13,659 $21,670 $0 $109,900 $34,021 $427,835 

(Over)/Under

Budget $36,415 $341 $41,330 $0 ($22,600) $9,357 $64,843 

FY15 

Carryover $32,908 CPI Decrease ($24,944) FY16 Carryover $72,807 

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Salary costs decreased due to successfully acquiring external (non-AMP) funds.

- Operating expenses decreased due to buying camera and software with FY15 funds.

- Funds to other USGS cost centers increased to provide salary for archival and transfer of legacy dataset of 

archeological site lidar surveys from 2006 to 2014.

- Carryover will be used to cover remote sensing analyses.
29

FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 5: Foodbase Monitoring and Research

Program Manager (PM) Theodore Kennedy Principal Investigator(s) 

(PI)

Theodore Kennedy, USGS, GCMRC

Jeff Muehlbauer, USGS, GCMRC

Charles Yackulic, USGS, GCMRC

Scott Miller, BLM/USU

David Lytle, OSU

Scott Wright, USGS, CWSC

Mike Yard, USGS, GCMRC

Email tkennedy@usgs.gov

Telephone (928) 556-7374

SUMMARY

Overview: Aquatic insects represent the primary prey for endangered humpback chub, rainbow trout, and 

countless other types of wildlife living in and along the Colorado River in Glen and Grand Canyons. The 

objectives of Project 5 are to: 1) determine why mayflies, caddisflies, and stoneflies are virtually absent from 

the Colorado River downstream of Glen Canyon Dam, 2) track the status and trends of the existing 

invertebrate foodbase, and 3) monitor rates of algae production.

Accomplishments: Our group completed a major data synthesis demonstrating that daily fluctuations in 

discharge associated with hydropeaking (load following) from Glen Canyon Dam are partially responsible for 

the absence of mayflies, stoneflies, and caddisflies from the Colorado River. This synthesis represents 

comprehensive work toward the majority of individual project elements outlined in Projects 5.1.1-8 and 5.2.1 

in the workplan. The results of this synthesis were published in the journal BioScience and are summarized in 

Figure 1. Additional work towards all of these project elements will continue into FY17. 

In our BioScience synthesis, we used multiple lines of evidence to determine how hydropeaking affects 

aquatic insect populations. One key line of evidence in this synthesis was the finding that 

Figure 1. Conceptual model of how hydropeaking affects aquatic insects. Aquatic insects are ubiquitous in freshwaters and are the primary prey for 

myriad species of wildlife living in and along rivers. These insects have complex life cycles that include a terrestrial winged adult life stage, whereas 

egg, larval, and pupal stages are aquatic. Ecologically important insect groups such as mayflies, stoneflies, and caddisflies cement their eggs along 

river-edge habitats, making them especially sensitive to hydropeaking and other dam water management practices that affect these edge habitats. 

Adapted from Kennedy and others (2016).
30

aquatic insect eggs experience high mortality when they are exposed to brief periods of desiccation (see 

Figure 2). These experiments were conducted by Scott Miller’s research group using eggs collected 

downstream of Flaming Gorge Dam. We also found that most aquatic insects tend to lay their eggs along river 

banks, where such desiccation occurs under hydropeaking. Another key line of evidence in the BioScience

synthesis came from our aquatic insect monitoring efforts in Grand Canyon. Since 2012 we have been 

monitoring the adult life stages of aquatic insects in Grand Canyon by collaborating with river guides, 

educational groups, and private boaters. Each night in camp, these citizen scientists deploy a simple light trap 

along the river edge. Using a dataset of over 2500 of these samples collected from 2012–2014, we 

demonstrated that midge abundance in Grand Canyon is affected by the timing of hydropeaking waves (see 

Figure 3). This research was highlighted in a perspectives essay published in Science

(http://science.sciencemag.org/content/353/6304/1099), the top scientific journal in the world. 

In FY16 our collaboration with citizen

scientists yielded 1,343 new light trap samples 

from throughout Grand Canyon towards 

Projects 5.1.1 and 5.2.1. In this fiscal year we 

also completed pilot egg laying studies in 

support of Project 5.1.5 throughout Glen 

Canyon, and throughout Marble and Grand 

Canyons during a river trip from October 7-24.

Figure 3. The timing of hydropeaking waves determines insect 

abundance in Grand Canyon. Hydropeaking waves released from the 

Dam propagate downstream, and at river miles 50 and 165 daily flow 

minima occur at dusk when insect egg laying occurs (a). Midge 

abundance peaks at these same river miles, because of variability in egg 

survival, with average abundance more than three times greater at 

locations where the daily flow minima coincide with peak egg-laying 

activity (b). Adapted from Kennedy and others (2016).

Figure 2. Aquatic insect eggs die after short periods of drying, such 

as along the banks of a hydropeaking river. Graph shows egg 

viability (number of hatched eggs/total eggs) after desiccation for 

eggs of (a) a type of mayfly (Baetis sp.), and two types of caddisfly 

(b: Brachycentrus; c: Hydropsyche). Adapted from Kennedy and 

others (2016).
31

Our group has also gained international recognition for the revolutionary improvements to aquatic 

invertebrate sampling in support of our research. These include sticky traps that can be rapidly deployed and 

analyzed, as evidence by the 1,832 sticky trap samples our group collected in Glen, Marble, and Grand 

Canyons in FY16 in support of Projects 5.2.1, 5.2.2, and 5.2.4. Sticky traps represent a cheap, and effective 

monitoring tool for assessing the condition of the aquatic foodbase (published in Marine and Freshwater 

Research, see Figure 4). We have also developed methods for quantifying the accuracy of invertebrate drift 

measurements (see Figure 5). This allows us to directly compare drift data from across rivers where different 

drift net deployment techniques are often required (i.e., staking nets to cobble bars in smaller rivers vs. 

deploying nets from a boat in larger rivers). This sampling issue previously prevented comparison of foodbase 

conditions across tailwaters, including across segments of the Colorado River downstream of Glen Canyon 

Dam. The results of this analysis are being published in the Canadian Journal of Fisheries and Aquatic 

Sciences. Using these new methods, our group collected 278 invertebrate drift samples from throughout Glen, 

Marble, and Grand Canyon in support of Projects 5.2.1-5. All these methods, including light traps, sticky 

traps, and drift, are included in the invertebrate sampling chapter for the new edition of the seminal 

textbook Methods in Stream Ecology. Thus, these new methods will likely become the standard for sampling 

aquatic invertebrates in rivers globally.

Significant progress has also been made towards the objectives of Project 5.3, Monitoring algae production in 

Glen, Marble, and Grand Canyon. A draft manuscript synthesizing controls of algae production in Glen 

Canyon is currently undergoing review (see Project 5.3.1). In collaboration with GCMRC’s water quality 

monitoring program we have continued collecting dissolved oxygen data from river miles 0, 30, 61, 89, 166, 

and 225; we now have 5-8 years of continuous data from each of these sites (see Project 5.3.2). In FY16, 

Charles Yackulic participated in a national USGS working group on estimating algae production from 

dissolved oxygen data. Through his involvement in this working group, new models for estimating algae 

Figure 5. Graph showing the relationship between filtration efficiency 

of drift nets (a measure of clogging) and the reliability of drift 

concentration estimates. A filtration efficiency of 1 represents an 

unclogged drift net. Adapted from Muehlbauer and others (In press).

Figure 4. Seasonal variation in abundance of midges in the Lees 

Ferry reach downstream of Glen Canyon Dam, grouped by sex for the 

year 2014. Height of bars represents the average midge catch per 

sticky trap (n=48 sticky traps deployed throughout Lees Ferry per 

sampling date). The error bars represent one standard error. Data for 

May (5/7) were likely biased low due to unseasonably windy and 

rainy weather. Adapted from Smith and others (2016).
32

production that are faster and more flexible have been developed (see Project 5.3.3). These algae production 

models are currently being implemented with our Colorado River data. 

Next Steps: The main conclusion from our BioScience synthesis was that it might be possible to mitigate 

negative effects of hydropeaking on aquatic insects by stabilizing flows every weekend during periods of 

peak insect activity. Our proposed flow experiment was also highlighted in the Science article mentioned 

above as an example of how minor tweaks to flow management policies have the potential to lead to major 

improvements in river health. Thus, next steps are to design a research and monitoring program specifically 

tailored to evaluating the effectiveness of ‘bug flows’. Regardless of when bug flows are implemented, we 

propose continued research and monitoring of the invertebrate prey base supporting humpback chub, rainbow 

trout, and native fish populations.

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Journ

al 

article

Deleterious effects of net 

clogging on the 

quantification of stream 

drift. 

Muehlbauer, J.D., Kennedy, 

T.A., Copp, A.J. & Sabol, T.A. 

(In Press) Deleterious effects of 

net clogging on the 

quantification of stream drift. 

Canadian Journal of Fisheries 

and Aquatic Sciences.

Book 

chapt

er

Macroinvertebrate drift, 

adult insect emergence and 

oviposition. 

Baxter, C.V., Kennedy, T.A., 

Miller, S.W., Muehlbauer, J.D. 

& Smock, L.A. (In Press) 

Macroinvertebrate drift, adult 

insect emergence and 

oviposition. Chapter 21 in: 

Methods in Steam Ecology (Eds 

F.R. Hauer & G.A. Lamberti), 

3rd edition.

Maga

zine 

article

Hydropower waves, insect 

eggs, and citizen science.

Kortenhoeven, E.W., 

Muehlbauer, J.D., & Kennedy, 

T.A. (2016). Hydropower waves, 

insect eggs, and citizen science.

Boatmen’s Quarterly Review 29: 

19-22.

Journ

al 

article

Incorporating temporal 

heterogeneity in 

environmental conditions 

into a somatic growth 

model.

Dzul, M.C., Yackulic, C.B., 

Korman, J., Yard, M.D. & 

Muehlbauer, J.D. (2016) 

Incorporating temporal 

heterogeneity in environmental 

conditions into a somatic growth 
33

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

model. Canadian Journal of 

Fisheries and Aquatic Sciences. 

DOI: 10.1139/cjfas-2016-0056

Journ

al 

article

Phenology and life history 

plasticity of the angel 

lichen moth (Cisthene 

angelus) in Grand Canyon, 

AZ, USA. 

Metcalfe, A.N., Kennedy, T.A. 

& Muehlbauer, J.D. (2016) 

Phenology and life history 

plasticity of the angel lichen 

moth (Cisthene angelus) in 

Grand Canyon, AZ, USA. The

Southwestern Naturalist. 61: 

233-240. DOI: 10.1029/SWNATD-16-00038.1

Journ

al 

article

Evaluating potential 

sources of variation in 

Chironomidae catch rates 

on sticky traps. 

Smith, J.T., Muehlbauer, J.D. &

Kennedy, T.A. (2016) 

Evaluating potential sources of 

variation in Chironomidae catch 

rates on sticky traps. Marine and 

Freshwater Research. 67: 1987-

1990. DOI: 10.1071/MF15189

Journ

al 

article

Flow management for 

hydropower extirpates 

aquatic insects, 

undermining river food 

webs. 

Kennedy, T.A., Muehlbauer, 

J.D., Yackulic, C.B., Lytle, 

D.A., Miller, S.W., Dibble, K.L., 

Kortenhoeven, E.W., Metcalfe, 

A.N. & Baxter, C.V. (2016) 

Flow management for 

hydropower extirpates aquatic 

insects, undermining river food 

webs. BioScience. 77: 561–575. 

DOI: 10.1093/biosci/biw059

Journ

al 

article

Prey size and availability 

limits maximum size of 

rainbow trout in a large 

tailwater: insights from a 

drift-foraging 

bioenergetics model.

Dodrill, M. J., Yackulic, C. B., 

Kennedy, T. A., & Hayes, J. W. 

(2016). Prey size and availability 

limits maximum size of rainbow 

trout in a large tailwater: insights 

from a drift-foraging 

bioenergetics model. Canadian 

Journal of Fisheries and Aquatic 

Sciences, 73(5), 759-772.

Journ

al 

article

Resource subsidies 

between stream and 

terrestrial ecosystems 

under global change. 

Larsen, S., Muehlbauer, J.D. &

Martí, E. (2016) Resource 

subsidies between stream and 

terrestrial ecosystems under 
34

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

global change. Global Change 

Biology 22: 2489–2504. DOI: 

10.1111/gcb.13182

Prese

ntatio

n

Flow management for 

hydropower extirpates 

aquatic insects, 

undermining river food 

webs.

TA Kennedy, May 3, 2016, Flow 

management for hydropower 

extirpates aquatic insects, 

undermining river food webs.

WebEx briefing for Glen 

Canyon Dam Adaptive 

Management Working Group.

Prese

ntatio

n

Flow management for 

hydropower extirpates 

aquatic insects, 

undermining river food 

webs.

TA Kennedy, April 29, 2016, 

Flow management for 

hydropower extirpates aquatic 

insects, undermining river food 

webs. WebEx briefing for 

Bureau of Reclamation, National 

Park Service, and US Fish and 

Wildlife Service staff.

Prese

ntatio

n

Flow management for 

hydropower extirpates 

aquatic insects, 

undermining river food 

webs.

TA Kennedy, April 21, 2016, 

Flow management for 

hydropower extirpates aquatic 

insects, undermining river food 

webs. WebEx briefing for 

Jennifer Gimble, Assistant 

Secretary for Water and Science.

Prese

ntatio

n

Hg and Se accumulation in 

the Colorado River food 

web

TA Kennedy, November 23, 

2015, Hg and Se accumulation in 

the Colorado River food web, 

Briefing for Lake Mead 

Ecosystem Work Group, Las 

Vegas, NV (invited)

Prese

ntatio

n

Hg and Se accumulation in 

the Colorado River food 

web

Walters, DW and TA Kennedy, 

October 21, 2015, Hg and Se 

accumulation in the Colorado 

River food web, Briefing for 

Technical Work Group, Glen 

Canyon Dam Adaptive 

Management Program, Phoenix, 

AZ.

Prese

ntatio

n

Longitudinal and temporal 

patterns of food 

availability for endangered 

Muehlbauer, J, T. Kennedy, E. 

Kortenhoeven, A. Metcalfe, 

November 2015 Longitudinal 
35

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

humpback chub, Gila 

cypha, in the Little 

Colorado river, Arizona

and temporal patterns of food 

availability for endangered 

humpback chub, Gila cypha, in 

the Little Colorado river, 

Arizona, Desert Fishes Council 

annual meeting, Death Valley, 

CA

Prese

ntatio

n

Little bugs, big data, and 

Grand Canyon.

Kennedy TA, J.Muehlbauer, D. 

Lytle, C.Yackulic, E. 

Kortenhoeven, A. Metcalfe, 

November 2015, Little bugs, big 

data, and Grand Canyon. Desert 

Fishes Council Annual Meeting, 

Death Valley, CA

Prese

ntatio

n

Flow management for 

hydropower extirpates 

aquatic insects, the 

foundation of river food 

webs.

Kennedy, TA, Muehlbauer JD, 

Yackulic CB, Lytle DA, Miller 

SW, Dibble KL, Kortenhoeven 

E, Metcalfe AN, Baxter CV. 

May 2016. Flow management 

for hydropower extirpates 

aquatic insects, the foundation of 

river food webs. Society for 

Freshwater Science Annual 

Meeting: Sacramento CA. 

Prese

ntatio

n

Dammed and adrift: 

patterns of invertebrate 

drift throughout Colorado 

River Basin tailwaters.

Muehlbauer, J.D., Kennedy, 

T.A., 2016. Dammed and adrift: 

patterns of invertebrate drift 

throughout Colorado River 

Basin tailwaters. Society for 

Freshwater Science Annual 

Meeting: Sacramento CA.
36

Project 5 Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $381,400 $12,500 $21,200 $29,800 $19,400 $50,635 $514,935 

Actual

Spent $342,738 $11,568 $39,224 $25,086 $19,038 $47,909 $485,563 

(Over)/Under

Budget $38,662 $932 ($18,024) $4,714 $362 $2,726 $29,372 

FY15 

Carryover $15,098 CPI Decrease ($26,071) FY16 Carryover $18,399 

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Salary costs decreased due to backfilling vacancies with lower graded personnel and receiving non-AMP 

funds.

- Operating expenses increased due to greater participation in citizen science program than expected.

- Carryover will be used to purchase microscope & imaging system and water quality monitors to measure 

algae production.
37

FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 6: Mainstem Colorado River Humpback Chub Aggregations and Fish Community Dynamics

Program Manager 

(PM) David Ward Principal Investigator(s) (PI)

David Ward, USGS, GCMRC

Mike Dodrill, USGS, GCMRC

Luke Avery, USGS, GCMRC

Brian Healy, NPS

Kirk Young, USFWS

Randy VanHaverbeke, USFWS

David Rogowski, AZGFD

Karin Limburg, State Uni. Of NY.

Email dlward@usgs.gov

Telephone (928) 556-7280

SUMMARY 

Project Element 6.1. Monitoring humpback chub aggregation relative abundance and distribution

During 27 August-13 September 2016, one mainstem river trip was conducted to monitor humpback chub 

with hoop nets and seines. This trip sampled fish within the boundaries of several known historic aggregations 

of humpback chub (i.e., LCR, Lava-Chuar-Hance, Bright Angel, Stephen Aisle, Middle Granite Gorge, 

Havasu, and Pumpkin), as well as sampling opportunistically at several localities outside of known 

aggregations (e.g., at a recently discovered group of humpback chub near river mile (RM) 35, and at several 

sites in western Grand Canyon where an increase in humpback chub densities have been detected). In 2015 

and 2016, the aggregation trips have also included seining of backwaters throughout Grand Canyon, and have 

deployed portable antennae technology. The primary purpose of these annual trips has been to construct a 

long term catch per unit effort (CPUE) index of humpback chub in the mainstem Colorado River, both within 

and outside of defined aggregation localities, in fulfillment of conservation measures. A major long term 

finding of this study has been that since 2006 there have been significant increases in CPUEs of humpback 

chub at most aggregation localities, as well as at non aggregation sites (Fig 1). Additionally, we have detected 

increases in the relative abundances of humpback chub stemming from translocation efforts into Shinumo and 

Havasu creeks, and have detected either new aggregations/populations of humpback chub (e.g., 35 Mile 

locality, western Grand Canyon), or detected expansion of previously known aggregations (e.g., 35 Mile, 

Shinumo, Havasu, Pumpkin). In 2016, we captured an unprecedented number of humpback chub in western 

Grand Canyon from all size classes (Figure 1). Data from these trips have also demonstrated that obtaining 

absolute abundance information is likely to be a very costly endeavor in terms of effort and expense should 

that avenue be pursued. Finally, these trips gather information on other members of the fish community. 
38

Figure 1. Catch per unit effort index of humpback chub captured in hoop nets from 1991-1993, 2002-2006, 2010-2013, and 2015. Note, 2016 data is 

still being analyzed. 

Project Element 6.2. Humpback chub aggregation 

recruitment studies

This Project element seeks to increase our understanding 

of humpback chub recruitment dynamics at wide-spread 

locations within the mainstem Colorado River using a 

variety of techniques including otolith microchemistry 

and traditional sampling techniques. Building on prior 

studies of water chemistry and otolith microchemistry of 

juvenile humpback chub, we collected water samples 

throughout the mainstem Colorado River and tributaries 

in order to identify isotopic or chemical signatures that 

may be used to identify areas of humpback chub 

spawning and recruitment. A suite of major, minor, and 

trace elements along with oxygen and carbon isotopes were analyzed. Although year to year variability is 

present, the mainstem Colorado River water is more “self-similar” throughout the canyon compared to 

tributaries. Tributaries with warmer more carbonated water tend to be elevated in heavy isotopes of both 
39

oxygen and carbon. Although we did not deliberately take any humpback chub for otolith microchemistry, a 

small number of incidental mortalities (10 fish less than 50mm total length), are available from 2016. We 

expect a report documenting preliminary findings from the otolith microchemistry in early 2017. Available 

findings, to date, show that stontium to calcium ratios are some of the best markers to discriminate between 

mainstem and tributary residency. Barium to calcium, magnesium to calcium, and zinc to calcium are also 

possible markers of tributary versus mainstem residency. However, these elements have shown elevated ratios 

in many fish species near the otolith core, likely related to incorporation of maternal fluids in the developing 

eggs, which may confound their use in this application. We continue to work with cooperators, such as the 

NPS, to collect and preserve any incidental mortalities that could contribute to this work.

Project Element 6.3. Monitoring mainstem humpback chub aggregations using PIT-tag antenna 

technology

We deployed 8 portable passive integrated transponder (PIT) tag antennas at 14 sampling locations during a 

September 2016 sampling trip to monitor humpback chub and other tagged fishes within or between known 

humpback chub aggregation localities (35 Mile, LCR, Tanner, Bright Angel [Schist Fist], Stephen Aisle, 

Middle Granite Gorge, above Kanab [Keyhole], Havasu, Fern Glen, 196 Mile, Fall Canyon, Pumpkin Spring, 

Bridge Canyon, and Surprise Canyon areas). These antennas detect tagged fish, including humpback chub and 

flannelmouth sucker; many that would otherwise go undetected at sampling locations. For example in 2016, 

372 humpback chub and 329 flannelmouth sucker were detected with the antennas, representing 42% and 

13% of the unique catches on the trip, respectively (Table 1). This technique represents an exciting new area 

of study to increase our understanding of the ecology and distribution of native fish in Grand Canyon. 

Additionally, we continued to collect genetic samples (small fin clips) from all humpback chub (excluding 

those from the LCR aggregation) to be analyzed by Wade Wilson (USFWS). Understanding the genetic 

make-up of fish in mainstem aggregations will provide information on relatedness and possibly identify areas 

of likely recruitment. Overall, the variety of sampling strategies and gears we used provides timely

information on the status of fish populations and informs decisions on both the operation of Glen Canyon 

Dam and non-flow actions. 

Table 1. Detections and percent detections of fish with hoop nets, PIT-tag antennas and with both gear types during mainstem aggregation trip 2016. 

BHS=bluehead sucker, BNT=brown trout, CRP=carp, *FBH=possible flannelmouth-bluehead hybrid, 

FMS=flannelmouth sucker, HBC=humpback chub, RBT=rainbow trout, UNK=unknown sucker. 

Project Element 6.4. System Wide Electrofishing

Goals and Objectives: The primary goal of the “System Wide Electrofishing” program is to monitor the 

status and trends of native and nonnative fish that occur in the Colorado River ecosystem via boat 

electrofishing from Lees Ferry to Lake Mead. Lees Ferry monitoring (Glen Canyon Dam to Lees Ferry) is 

BHS BNT CRP FBH* FMS FRH** HBC RBT UNK Total

Captures 4 0 4 5 2,096 2 451 0 0 2,562

% of Total 80% 0% 50% 100% 82% 67% 51% 0% 0% 74%

Contacts 1 1 4 0 329 1 372 3 91 711

% of Total 20% 100% 50% 0% 13% 33% 42% 100% 100% 21%

Cap/Contact 0 0 0 0 119 0 62 0 0 181

% of Total 0% 0% 0% 0% 5% 0% 7% 0% 0% 5%

Total (n) 5 1 8 5 2,544 3 885 3 91 3,454

Species

Hoop Net Only

Antenna Only

Antenna and Hoopnet

Unique PIT Tag Contacts/Captures by Gear
40

discussed in a different subsection below. The purpose of this program is to obtain a representative sample of 

the fish community within the Colorado River. Results (species composition and relative abundance measured 

as CPUE) from our surveys can be used to interpret trends in abundance and distribution of native and 

nonnative fish within this reach. As humpback chub are not adequately sampled with electrofishing gear and 

no other program conducts a system wide monitoring program for this species we added a hoop net sampling 

component to our monitoring. In addition during sampling trips, once below the Little Colorado River inflow 

we use angling to sample for catfish each evening at camp. 

Summary of progress:

In 2016 we completed three mainstem sampling trips. A stratified random sampling approach was used to 

obtain a representative sample of the river’s fish community that was susceptible to electrofishing or baited 

hoop nets. In the two spring/summer system wide trips approximately 639 sites were electrofished with 4,031 

fish captured. During the fall sampling trip from Diamond Creek to Pearce Ferry Rapid electrofishing was 

hampered by high levels of turbidity (>4,000 NTUs), thus we set more hoop nets (81 nets set) and did 

minimal electrofishing (22 sample sites). In total 319 hoop nets were set during the three trips capturing 1,561 

fish. Flannelmouth suckers dominated the catch for both electrofishing and hoop nets, with 55 and 72% 

percent of the fish captured respectively. We captured 179 humpback chub via baited hoop nets and the 

results are presented in the figure below (Figure. 1).

Monitoring activities funded (boat electrofishing/hoop net trips):

• Spring trip I: 6-21 April 2016

• Spring trip II: 19 May – 3 June 2016

• Diamond Down trip: 7-11 October 2016

Figure 2. Catch per unit (fish/hour) of humpback chub captured via baited hoop nets (n=319) in 2016 by river mile (RM) from Arizona Game and Fish 

Department system wide sampling of the Colorado River from Lees Ferry (RM 0 to Pearce Ferry Rapid RM 281.4)

Summary of trends:

-0.05

0.05

0.15

0.25

0.35

0.45

0.55

0 50 100 150 200 250

Humpback Chub

Catch per unit effort (fish/hour)

River mile
41

Nonnative rainbow trout continue to dominate the fish community within Lees Ferry and Marble Canyon 

reaches of the Colorado River and begin declining in abundance (e.g. lower CPUE) near the Little Colorado 

River confluence. Native fish (flannelmouth sucker and speckled dace) begin dominating the fish community 

downstream of the confluence with the Little 

Colorado River. In general, reach wide catch rates 

for most fish species remained stable over the 

past five years (no statistically significant trends), 

with the exception of rainbow trout. Rainbow 

trout CPUE has significantly declined over the 

past three years. Hoop netting results revealed 

that humpback chub are quite common below 

Diamond Creek (river mile 225) to Pearce Ferry 

Rapid (RM 281.4). All age/size classes were 

represented and all humpback chub captured in 

the reach (below RM 225) were untagged (no 

recaptures) with the exception of two fish in our 

fall sampling. These two recaptures were initially tagged by USFWS a month previous below RM 225. The 

numbers and CPUE of humpback chub caught below RM 225 is equivalent to what we see around the Little 

Colorado River. These results indicate that these humpback chub are not utilizing the Little Colorado River or 

any of the traditional “aggregation sites” (Valdez and Ryell 1995), where 50-80% of the humpback chub 

captured are recaptures.

Rainbow Trout Monitoring in Glen Canyon

Goals and Objectives: The goal of “Rainbow Trout Monitoring in Glen Canyon” is to monitor the status and 

trends of rainbow trout abundance and distribution in the Colorado River reach between Glen Canyon Dam 

and Lees Ferry. Boat electrofishing is utilized to obtain a representative sample of the fish community within 

this reach. The general objectives are to monitor the trout fishery to determine status and trends in relative 

abundance (catch per unit effort), population structure (size composition), distribution, reproductive success, 

growth rate, relative condition (Kn) and overall recruitment to reproductive size in response to Glen Canyon 

Dam operations. In addition, we conduct one night of nonnative sampling in July within this reach to monitor 

nonnative species.

Summary of progress: We completed three sampling trips in 2016, sampling 113 standard sites in total and 

capturing 2145 fish (excluding the nonnative sampling). During nonnative sampling in July of 2016 we 

captured three Walleye and did not capture any Green Sunfish in the slough at river mile -

12.

Monitoring activities funded (boat electrofishing trips):

• Spring trip: 15-18 March 2016, 36 standard sample sites

• Summer trip: 18-22 July 2016, 40 standard sample sites, plus an additional 11 sites for nonnatives

• Fall trip: 13-16 September 2016, 42 standard sample sites

Summary of trends: Rainbow trout continue to dominate the fish community within the Lees Ferry reach, 

comprising 94.8% of the catch (standard electrofishing), with brown trout comprising 3.3 % of the catch, 

compared to 2.1 and 0.55% in 2015 and 2014 respectively. The increase in brown trout during these years was 

primarily from one age class, young of the year. Typically in past years we caught very few brown trout with 

most of those as adults. This increase in recruitment over the past three years is unusual. It is currently unclear 

what causative factor or factors are related to this increase in brown trout. Potential causes identified to date 

include direct and indirect effects of reduced rainbow trout density since late 2014, growth and maturation 
42

facilitated by abundant food resources in the form of young trout prior to this decline, improved spawning and 

rearing conditions due to 2012, 2013, and 2014 fall high flow events, or some combination of these or other 

unidentified factors. Currently there is little evidence to support any one hypothesis concerning changes in 

brown trout abundance in the Lees Ferry reach. 

Rainbow trout have maintained a self-sustaining population since the mid-1990s. Relative abundance, as 

measured by electrofishing CPUE, has fluctuated greatly since AGFD began standardized sampling in 1991. 

CPUE of rainbow trout was the highest ever recorded in 2011–2012, but has declined since 2012. In addition, 

the percent of large rainbow trout in the system has declined as has the median size of reproductively active 

trout. This suggests there were more rainbow trout in the system (based on higher CPUE) than the system was 

able to maintain during 2011-2014, from a limited food base. Relative fish condition (Kn) for rainbow trout 

reached a record low (~ 0.8) in fall of 2014, and has been increasing since then, concurrently with the 

decrease in relative numbers of rainbow trout. Condition of rainbow trout in 2016 has been very good with 

some of the highest levels of condition (~1) in adult (12 to 16 inches) and big fish (Kn~ 1.1: > 16 inches) 

observed in the past 25 years. While the percent young of the year (YOY) in the fall catch was relatively high 

(87%), the CPUE of YOY was only 1.85 fish/hour, thus not at levels of concern (as in 2011). 

Project Element 6.5. Brown trout natal origins through body pigmentation patterns in the Colorado 

River

This project was not funded in the FY15–17 triennial work plan. 

Project Element 6.6. Mainstem translocation of humpback chub

Funded in FY17- Discussion will occur at December cooperators meeting about implementation of this 

project

Project Element 6.7 Rainbow Trout Early Life Stage Surveys

Goals and Objectives: The primary objective of the RTELSS study is to monitor the response of the age-0 

population of Rainbow trout in Lees Ferry to variations in Glen Canyon Dam operations and to naturally 

occurring disturbances to the Colorado River in Glen Canyon.

Summary of progress: Field activities for the Rainbow Trout Early Life Stage Survey (RTELSS) in 2016 

consisted of redd surveys for estimation of spawning magnitude, and electrofishing sampling for estimation of 

population dynamics. Due to staffing vacancies, the normal sampling schedule for this project was truncated 

from 11 redd surveys conducted in previous years to 5 surveys. However, surveys were scheduled monthly 

over historic peak spawning times to best capture changes in redd abundance and distribution. 

Summary of trends:

Redd Surveys

Five redd surveys were conducted from February 2016 through May 2016. We observed 2,087 redds and 

generated an overall estimate of 1,893 redds created for the season. The magnitude and patterns of redd 

distribution was similar to past years, although the peak was a couple weeks later than is typical. In past years 

the peak has occurred around mid to late March or early April. The peak in distribution for 2016 appeared to 

be mid-April, but there is some uncertainty about the exact timing of the peak due to fewer sampling 

occasions (Table 1).
43

Table 2. Dates of the 5 redd surveys conducting in 2015 and the number of redds observed for each of those surveys.

Redd Surveys for 2016

Date of Survey

Number of 

Redds 

Observed

2/19/2016 58

3/17/2016 538

4/11/2016 616

5/2/2016 503

5/24/2016 372

In most years the “zero” count (count low enough to be considered the end of the spawn) for the tail end of 

the distribution doesn’t occur beyond June. Due to logistical constraints, resources were allocated to 

electrofishing efforts in June and not additional redd surveys. In addition to the late peak in redds observed in 

mid-April, we observed a relatively high number of redds late into May. This suggests the spawn may have 

continued later in the season than previously observed, possibly the result of late developing spawning adults.

Electrofishing Surveys

Four electrofishing surveys were conducted in 2016. Age-0 population estimates for June, July, August, and 

November are 147,000 (47,000 Lower Confidence Interval (LCI); 56,000 Upper Confidence Interval (UCI)), 

367,000 (77,000 LCI; 82,000 UCI), 183,000 (34,000 LCI, 33,000 UCI)), and 34,000 (10,000 (LCI); 10,000 

(UCI)) respectively. No survey was conducted in September due to logistical constraints. Population estimates 

for July were much higher than seen in previous years, similar to what was observed in 2012. 

Project Element 6.8. Lees Ferry Creel Survey

Goals and Objectives: The cold tailwater below Glen Canyon Dam is an important recreational fishery for 

rainbow trout. The goal of the “Lees Ferry Angler Surveys” project is to monitor the status of the fishery and 

estimate angler use by conducting angler surveys to obtain a representative sample of the recreational angling 

community that utilizes this resource. AGFD uses a stratified random sampling approach to select a subset of 

days for interviews, of both boat and shoreline anglers. Information obtained includes but is not limited to 

catch rates, gear type, species composition, harvest, and satisfaction with angling experience. 
44

Summary of progress: As of this report, we have collected data for 

2016 up to 20 October 2016. Data for October through December 2016 

will be analyzed and included in our annual report, to be submitted in 

2017. Sampling days were stratified by month (6 days) and by weekday 

(2 days) and weekend (4 days). As of the end of October 2016 we have 

conducted angler surveys on 60 days, and interviewed 1,106 anglers. 

From June 2015 to June 2016 a game camera was installed at Lees 

Ferry recording images of the boat launch area to provide a better 

estimate of boat anglers for the days and hours when we do not have a 

technician present.

Summary of trends: As of the end of October 2016, rainbow trout 

CPUE levels for boat anglers was significantly less in 2016 (0.668 

fish/hour) compared to 2015 (1.31)(matched paired T-test by month; P 

= 0.0022). Average boat angler CPUE for rainbow trout to date was 

0.668 fish/hour and 0.197 fish/hour for the walk-in area (n=953 and 

153 respectively). Both values represent relatively large reductions in 

CPUE compared to the record highs observed 2011–2014 (> 2.0 fish/hour).

As of 30 October 2016, 71.8% of the interviewed anglers were from Arizona and the rest from out of state (or 

country). Almost half (49.6%) of the boat anglers interviewed used a guide. 

For calendar year 2015 we conservatively estimated about 8,450 angler use days for the Lees Ferry fishery. 

Angler use is defined as one angler fishing one day, regardless of the length of time spent that day. There has 

been a significant decline in angler use of the fishery since 2002. Despite angler satisfaction remaining high 

with a score of 3.95, and 3.15 (on a scale of 0-5) for boat and walk-in anglers respectively, angler satisfaction 

has declined in the past three years. Based on a preliminary analysis of our game camera data we are 

underestimating boat angler use by 32 and 38 % by weekday and weekend respectively. Based on the game 

camera data the boat angler use estimate would increase from 5,954 [5103, 6805] to 7,999 [7148, 8851].
45

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Journal 

Article

Effects of Increased 

Discharge on Spawning 

and Age-0 Recruitment of 

Rainbow Trout in the 

Colorado River at Lees 

Ferry, Arizona. 

Aug. 2015

Avery, L. A., Korman, J., 

and Persons, W. R. (2015) 

Effects of Increased 

Discharge on Spawning and 

Age-0 Recruitment of 

Rainbow Trout in the 

Colorado River at Lees 

Ferry, Arizona. North 

American Journal of 

Fisheries Management 35: 

671-680

Report

Colorado River Fish 

Monitoring in Grand 

Canyon, Arizona – 2015 

Annual Report.

Feb

2016 Report

Rogowski, D.L., R.J. 

Osterhoudt, L.K. Winters, 

and P.N. Wolters. Colorado 

River Fish Monitoring in 

Grand Canyon, Arizona –

2015 Annual Report.

Report

Status of the Lees Ferry 

Rainbow Trout Fishery 

2015 Annual Report

March 

2016 Report

Winters, L.K., D.L. 

Rogowski, and P.N. Wolters. 

Status of the Lees Ferry 

Rainbow Trout Fishery 2015 

Annual Report

Thesis

Use of ultrasonic imaging 

to evaluate egg 

maturation of humpback 

chub Gila cypha

Oct 2016

Brizendine, Morgan 2015. 

Use of ultrasonic imaging to 

evaluate egg maturation of 

humpback chub Gila cypha . 

MS Thesis, University of 

Arizona

Journal 

Article

Economic Value of 

Angling on the Colorado 

River at Lees Ferry: 

Using Secondary Data to 

Estimate the Influence of 

Seasonality. 

Oct 2016

Bair, L.S., D.L. Rogowski, 

and C. Neher. 2016 

Economic Value of Angling 

on the Colorado River at 

Lees Ferry: Using Secondary 

Data to Estimate the 

Influence of Seasonality. 

North American Journal of 

Fisheries Management 

36:6 1229-1239
46

Project 6 Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $180,100 $5,700 $21,200 $290,000 $0 $33,505 $530,505 

Actual

Spent $143,030 $2,838 $15,323 $265,057 $3,743 $27,267 $457,258 

(Over)/Under

Budget $37,070 $2,862 $5,877 $24,943 ($3,743) $6,238 $73,247 

FY15 

Carryover $33,821 CPI Decrease ($26,859) FY16 Carryover $80,209 

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Salary costs decreased due to vacancies. 

- Cooperative agreements decreased due to coops funded from another project. 

- Carryover will be used to offset FY17 shortage.

Open 

File 

Report

Colorado River Fish 

Monitoring in Grand 

Canyon, Arizona. 2002-

14 Humpback Chub 

Aggregations. USGS 

Open File Report. 

Dec. 2016

Persons, W. R., D. R. Van 

Haverbeke, and M. J. 

Dodrill. 2016. Colorado 

River Fish Monitoring in 

Grand Canyon, Arizona. 

2002-14 Humpback Chub 

Aggregations. USGS Open 

File Report.
47

FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 7: Population Ecology of Humpback Chub in and around the Little Colorado River

Program Manager 

(PM) Charles Yackulic Principal Investigator(s) (PI)

Charles Yackulic, USGS, 

GCMRC

Kirk Young, USFWS

Kim Dibble, USGS, GCMRC

Mike Yard, USGS, GCMRC

Maria Dzul, USGS, GCMRC

David Rogowski, AZGFD

Randy VanHaverbeke, USFWS

Dennis Stone, USFWS

David Ward, USGS, GCMRC

Jeff Muehlbauer, USGS, GCMRC

Josh Korman, EcoMetric 

Research

Ted Kennedy, USGS, GCMRC

Email cyackulic@usgs.gov

Telephone (928) 556-7379

SUMMARY

Introduction

The overall objectives of this project are to track the current status of humpback chub populations and to 

continue to improve our ability to predict how dam management and other management actions, as well as 

other important sources of variation, will affect humpback chub populations dynamics, and ultimately adult 

abundances. 

Background

A well-designed mark-recapture monitoring program has been in place in the Little Colorado River (LCR) 

since the fall of 2000, led by US Fish and Wildlife Service. An adequate monitoring program of humpback 

chub in the Colorado River around the LCR took longer to develop and lack of such a program hindered 

earlier attempts to understand the impacts of dam management (i.e., 2000 LSSF experiment) and nonnative 

fish removal (2003–2006) on humpback chub population dynamics. In particular, it was recognized that more 

emphasis needed to be placed on the dynamics of smaller size classes (~40-100 mm) of humpback chub in the 

CR. Starting in 2009, the Near Shore Ecology (NSE) project developed a framework for monitoring that has 

since been continued as the Juvenile Chub Monitoring (JCM) project. Since 2012, we have developed models 

that integrate data collected in the LCR with data collected by the JCM and NSE projects to provide a holistic 

picture of the humpback chub population dynamics (Yackulic and others, 2014). This work has illustrated the 

importance of variation in vital rates between the LCR and CR, as well as important movement phenomena 

(e.g., skip-spawning) that biased previous attempts to estimate adult abundance because of a population 

modelling issue known technically as “temporary emigration.” (In short, the majority of adult humpback chub 

are captured during spawning in the LCR, however, some proportion of adults chose not to spawn every year 

and this is known to lead to negative biases in abundance estimates). While the multistate approach to 

population modelling addresses this issue, there are other potential sources of biases and uncertainties (in 

particular, long-term hoop net avoidance) that we are seeking to address through new technologies and new 

modelling approaches.
48

One of the primary goals of this project is to improve our ability to forecast humpback chub population 

dynamics and inform management decisions. In support of the LTEMP process, we integrated versions of this 

humpback chub population model with models of rainbow trout population dynamics to provide predictions 

under various management alternatives and including various uncertainties (Yackulic, Korman, and Coggins 

– LTEMP appendix; Runge et al., 2015). Critical examination of simulations used in LTEMP provides 

important clues as to important areas of uncertainty in forecasting population dynamics of humpback chub 

(and rainbow trout), and thus important areas for research. In particular, uncertainty in juvenile production 

and outmigration plays an important role, as does uncertainty in rainbow trout flow-recruitment relationships. 

Uncertainty in relationships between temperature and humpback chub population dynamics was less 

important in LTEMP simulations because the LTEMP alternative did not differ in their implications for 

temperature (i.e., under LTEMP alternatives temperature was a random variable that was the same across 

alternatives, as opposed to something that was actually managed in any alternative). Nonetheless, we expect 

that changes in water temperature and other aspects of water quality (turbidity, nutrients) that are related to 

dam management decisions and broader drivers (Quagga, climate, structural deficit, etc.) will likely be one of

the dominant drivers of future humpback chub population dynamics. In addition, recent research in 

collaboration with Lucas Bair has revealed the potential importance of uncertainty in various humpback chub 

vital rates in determining efficient trout removal triggers (including whether trout removal is necessary – See 

Project 13.3). 

Specific goals of this project in the triennial work plan are to:

1) Monitor humpback chub in the lower 13.6 km of the LCR and Colorado River reference site (river 

mile (RM) 63.0-64.5) 

2) Estimate recruitment and outmigration from the LCR by marking juvenile humpback chub 

throughout the lower 13.6 km of the LCR in July. 

3) Develop field and analytical techniques to better use remote technologies for detecting passive 

integrated transponder (PIT) tags to address questions of trap avoidance and to potentially minimize 

future handling of chub. 

4) Test new non-lethal tools for measuring the health and condition of humpback chub in the field. 

5) Undertake targeted, cost-effective research to understand mechanisms underlying observed 

population processes, including the roles of high CO2 at base flow, gravel limitation, parasites, and 

the aquatic food base. 

6) Continue to develop models that integrate findings from the above projects and provide meaningful 

predictions to guide adaptive management. 

Key hypotheses being tested include:

1) To what extent, do rainbow trout affect the growth and survival of juvenile humpback chub, and 

ultimately humpback chub adult abundances?

2) To what extent, does temperature affect the growth and survival of juvenile (and older size class) 

humpback chub, and ultimately humpback chub adult abundances

3) To what extent, does translocation of humpback chub population augment the adult population of 

humpback chub?

4) To what extent, are humpback chub dynamics in the Colorado River, driven my conditions in the 

LCR? In particular, how does juvenile production and outmigration from the LCR vary and what are 

the drivers of this variation?
49

5) To what extent, do other physical (turbidity and nutrients) and biological (primary production, 

insect densities) factors drive humpback chub population dynamics?

6) Are estimates of adult humpback chub abundances biased because older, larger humpback chub 

avoid hoopnets (i.e., is there long-term trap avoidance behavior)?

7) Are estimates of adult humpback chub abundances biased because of unmodelled heterogeneity in 

skip-spawning rate and/or heterogeneity in detection probability?

Summary of activities and results from various project elements Field Sampling

Spring and fall monitoring in the LCR

Based on data from the spring trips, the population of humpback chub ≥150 mm in the lower 13.6 km of the 

LCR was estimated to be 4,850 (Standard Error (SE) = 376) and the adult population (≥200 mm) was 

estimated to be 3,974 (SE = 314). These numbers represents a slight increase compared to the significant 

decline observed in spring 2015, however the point estimates remain lower than any estimates since 2007. In 

the fall it was estimated that there were 4,053 (SE = 232) Humpback Chub ≥150 mm in the lower 13.6 km of 

the LCR, of which 1,665 (SE = 132) were adults.

JCM monitoring in the CR

Preliminary estimates of humpback chub juvenile survival suggest reasonably high annual survival, but with 

high uncertainty. Fish condition for adult humpback chub (>200 mm) was poor throughout 2016 and has been 

since mid-2014 and is likely linked to lower abundances of spawning adults in the last two springs in the 

LCR. More thorough analyses of abundances and survival across size classes are ongoing. 

Pre-monsoon juvenile chub survey in the LCR

Juvenile humpback chub abundances were extremely low in 2016 (3,000 - SE = 500) compared to 2013 

(16,000 - SE = 2,400), 2014 (9,000 – SE = 700) and 2015 (25,000 – SE = 2,500). As a result, juvenile 

outmigration into the mainstem 

was likely very low this year, 

however, we are still analyzing 

these data. 

Development of models and field 

approaches to PIT antennae

Use in the LCR

Using a combination of Natal 

Origins data and PIT array 

detections in the LCR, we 

developed a model that estimates 

that hundreds of rainbow trout 

overwintered in the LCR during 

the winter of 2013–2014. The PIT 

array in the LCR continues to 

function, however there are 

indications that it may only function fully for 1-2 more years. We are beginning to explore cheaper 

alternatives for replacing the PIT array in future years that may provide as good or better information. A 

paper detailing the model and results was recently submitted for publication. USFWS has already experiment 

with portable antennas with good success.
50

Use in the JCM reach of the Colorado River

Whereas JCM monitoring was designed for monitoring early life stages of humpback chub, it has always 

detected very few adults, one factor that leads to high uncertainty in humpback chub adult abundances. 

During the September JCM trip we employed portable antennas in the Colorado River for the first time with 

the hope of improving detection of larger adults that may avoid hoopnets or the habitats in which hoopnets 

can easily be deployed. The early results are promising. These antennas detected more than 4 times as many 

unique adults as compared to hoopnets, including 16 adult humpback chub that have not been detected 

anywhere within the system in the last eight years. We are working to integrate these data into our population 

models.

Determining the utility of Bioelectrical Impedance Analysis (BIA) analysis

The purpose of this project was to determine the effectiveness of Bioelectrical Impedance Analysis (BIA), a 

nonlethal technique used in many other fish species, for estimating physiological condition of humpback chub 

(and related species). We completed laboratory trials using hatchery-raised humpback chub, bonytail, and 

roundtail chub in FY15 and prepared a manuscript in FY16, which is currently under review. Although fish 

exhibited low mortality using BIA, it did not substantially improve our estimates of fish condition beyond 

those generated using accurate length and wet mass measurements. However, in the absence of wet mass data, 

or when wet mass measurements are highly erroneous (due to environmental factors such as high wind or 

water on the scale), BIA became a more reliable tool for estimating fish condition. 

Research into mechanisms underlying population dynamics

Asian tapeworm monitoring

Tapeworm monitoring was conducted in the LCR at Boulders camp from May 23-26, 2016. Of 36 humpback 

chub treated for tapeworm, only 10 were found to be infected with a total burden of only 17 Asian tapeworms 

(a mean of 1.7 per fish). Infestation rate of humpback chub in the LCR has been very low for the last 2 years 

and appears to be much lower than was found during 2005–2007 sampling. All fish were released alive 

following treatment. 

LCR Foodbase Research

In 2016, the foodbase research group made five, four-day trips into the LCR, concurrent with USFWS and 

GCMRC humpback chub monitoring trips in April, May, June, September, and October in order to better 

understand links between food availability and humpback chub population dynamics and growth. Objectives 

and sampling effort for these trips were consistent with previous efforts in 2014 and 2015, including sticky 

trap sampling of adult emergent aquatic insects, benthic sampling of aquatic invertebrate larvae, and light trap 

sampling at the four camps. Data from previous efforts was used to show the strong links between food 

availability and humpback chub growth in the LCR (Dzul et al., 2016 CJFAS). We plan to submit an insectfocused journal article in FY17.

Potential for CO2 limitation

CO2 concentrations have been measured within the LCR from Horse Trail (RKM 30) to the confluence with 

the Colorado River using a variety of techniques and are known to be extremely high between Blue Springs 

(RKM 20.8) and RKM 16 (but lower in the small perennial flow about Blue Springs and in the lower LCR). 

There is some disagreement in actual CO2 concentrations, with electronic probes suggesting lower 

concentrations than titration methods, however, these general trends remain. As part of this project element, 

laboratory studies evaluated native and nonnative fish tolerance to high CO2 levels for both juvenile and adult 
51

fishes. Rainbow and brown trout had the lowest CO2 tolerances (90 and 100 mg/l respectively) and bullhead 

catfish (200 mg/l) and fathead minnow (256 mg/l) had the highest tolerance with native fishes being 

intermediate. Humpback chub eggs hatched and larval fish survived at CO2 levels below 25 mg/l (RKM 14), 

but deposition of calcite and suffocation of eggs may play a larger role in fish recruitment than actual CO2 

concentration. CO2 tolerance of all of the fishes we tested appear to be able higher than CO2 levels naturally 

found within the lower 16 km of the LCR. It does not appear likely that CO2 dynamics control fish 

populations in this area.

Model development

A paper detailing an improved statistical model for estimating effects of environmental factors on growth and 

applying the approach to understand drivers of growth in sub-adult humpback chub was published in CJFAS. 

We found that food availability and temperature were the primary drivers of growth in the LCR and turbidity 

and temperature played equal roles in humpback chub growth in the JCM reach. Another paper developing a 

novel approach for estimating abundance from the PIT array and ancillary data was submitted to CJFAS and 

estimates that a few hundred rainbow trout entered the LCR during the winter of 2013-2014. While rainbow 

trout have occasionally been found in the LCR, these results suggests that rainbow trout seasonal use of the 

LCR may be much greater than previously assumed. A manuscript detailing a joint mark-recapture model for 

juvenile humpback chub and rainbow trout is in the final stages of preparation and is expected to be submitted 

in early 2017. The model accounts for various sources of uncertainty (uncertainty in rainbow trout 

abundances, uncertainty from un-modeled environmental covariates, effects of environmental factors 

including turbidity and temperature) and estimates a statistically significant, negative effect of rainbow trout 

on humpback chub survival. The effect is moderate in comparison to other potential drivers (e.g., 

temperature), but is sufficient to affect long-term humpback chub population dynamics and adult abundances. 

Estimates from this model are being used as part of project 13.3 to develop tools for supporting management 

decisions in an effort led by Lucas Bair.

Synthesis and next steps

The population dynamics of humpback chub are relatively slow, particularly in the Colorado River. As a 

consequence, recruitment failure in one or a few years should not lead to an overreaction from managers, as a 

few bad years can quickly be erased by a couple very good years. On the other hand, if the status of the 

population declines to a point that is unacceptable due to inaction, the population will be slow to recover and 

may require much more intensive management interventions. Poor juvenile recruitment this year is 

particularly unfortunate because rainbow trout abundances in the Colorado River near the LCR confluence are 

currently quite low, and humpback chub juvenile survival is directly linked to rainbow trout abundances 

(Yackulic et al., in prep). Thus we are currently in a window to add humpback chub after many years of high 

rainbow trout abundances, when juvenile chub survival was low (despite fairly good recruitment to the 

Colorado River). Previously, it has been hypothesized that poor humpback chub recruitment years in the LCR 

are associated with lack of flooding during the Jan. 1 to May 31 seasonal window (Van Haverbeke et al., 

2013). Flooding in 2016 occurred relatively early in this window, but was greater in magnitude than in some 

years that have had good recruitment, in disagreement with this hypothesis. Furthermore, past estimates of 

humpback chub recruitment in the LCR occurred after monsoons and thus conflated two processes–juvenile 

recruitment and outmigration during the monsoons (when most outmigration occurs – Yackulic et al., 2014). 

It is now clear that there is substantial variation in both these processes. Over the four years of pre-monsoon 

surveys there has been substantial variation in juvenile recruitment, and over the eight years of study in the 

JCM there has been considerable variation in juvenile recruitment (juvenile recruitment to the JCM reach 

represents a portion of the outmigration from the LCR). Since recruitment and outmigration rates play such 

substantial roles in humpback chub population dynamics and may determine whether some management 
52

actions, like mechanical removal, are even necessary and if necessary how they should be timed to maximize 

chub benefits, we plan to continue the pre-monsoon surveys both in FY17 and the next work plan.

Trends in adult humpback chub over the last two and a half years are not good. Fish condition of adult 

humpback chub in the JCM reach has been poor and fewer adults have spawned in the last two years than in 

any period since 2007. Since detection probabilities for adults are low in the mainstem, it is not clear whether 

lower spawner abundances reflect a decline in actual adult abundances system-wide, or merely a decline in 

spawning rates (i.e., a lower proportion of adults have chosen to spawn). PIT-tag antennas deployed in the 

mainstem show great promise and may soon provide us with data to distinguish these hypotheses. We plan to 

work on developing models to understand temporal variation in skip-spawning rates in FY17 and in the next 

work plan. Recent declines in adult condition (and perhaps lowered rates of spawning) have likely been 

driven by a declining foodbase. Decreased invertebrate drift suggested much lower food availability in 2015 

and 2014 as compared to 2012 and 2013. 2016 data is still being processed. In turn, preliminary estimates 

suggest that gross primary production in Marble Canyon, estimated from dissolved oxygen, may have been 

lower in recent years as compared to 2013 and 2014, suggesting a bottom-up decline, ultimately driven by 

factors related to the nutrient concentrations of water released through Glen Canyon Dam. A primary focus of 

research in FY17 and proposed research in the next work plan will be to better understand how nutrients and 

other aspects of releases from Glen Canyon Dam affect primary production and determine whether these 

affects cascade up through the food web, ultimately affecting condition and population dynamics of both 

rainbow trout and humpback chub. 

Over the last two years, we have explored a number of hypotheses related to fish population dynamics in the 

LCR. CO2 limitation does not appear to be as big a factor as previously believed–a manuscript on these 

results will be submitted in 2017. Therefore, we do not expect the need for further research on this topic in the 

next work plan. With respect to Asian tapeworm monitoring, more years of data are needed to determine how 

infestation rates vary and whether they impact humpback chub dynamics over longer time spans. This 

monitoring is relatively cheap and will likely be proposed to continue in the next work plan, perhaps with 

additional work in the mainstem. We have found that seasonal and spatial patterns in food availability are 

likely linked to spatio-temporal variation in humpback chub growth and abundances, however, data are still 

being analyzed to determine if there is inter-annual variation. Intensive field work associated with this project 

is complete. We may, however, propose a downscaled version of monitoring associated with ongoing fish 

monitoring projects in future years. 

We have seen enormous gains in our understanding of humpback chub dynamics in the Colorado River 

around the LCR coinciding with the establishment of the JCM study area, including an ability to link 

management actions and environmental variation to population processes. This understanding of population 

dynamics and drivers allows us to predict how the quantity managers are primarily interested in, humpback 

chub adult abundances, will respond to management actions and environmental variation (i.e., the modelling 

framework developed for LTEMP by Yackulic, Korman, and Coggins). Recently, there have been signs that 

humpback chub populations are increasing in other parts of Grand Canyon, however, we have little to no 

understanding of what is driving these increases, and if, or how, we can sustain these increases. If we could 

understand the factors driving these increases and determine that there was a distinct population from the 

LCR aggregation, this could potentially radically change management of humpback chub downstream of Glen 

Canyon Dam. For these reasons, and given the success of the JCM/NSE approach, we propose to explore 

JCM-like sampling at a fixed site in western Grand Canyon in FY17 and the next work plan.
53

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Journal 

Article

CB Yackulic, et al. (in prep) 

Joint mark-recapture 

population modeling of 

interacting species

2017

Journal 

Article

L Bair, CB Yackulic, et al., (in 

prep) Enhancing native 

species population viability via 

cost-effective invasive species 

control in the Grand Canyon, 

USA.

2017

Journal 

Article

JD Muehlbauer, TA Kennedy, 

CB Yackulic, & EW 

Kortenhoeven (in prep) Dual 

light controls on aquatic insect 

densities throughout a large 

river.

2017

Journal 

Article

MC Dzul, CB Yackulic, J 

Korman, and T Andrews.

(submitted) Estimating animal 

abundance using continuous 

detection data from PIT arrays 

placed near the confluence of 

two rivers. Canadian Journal 

of Fisheries and Aquatic 

Sciences.

2017

Journal 

Article

KL Dibble, M Yard, DL Ward, 

and CB Yackulic. (in review) 

Does bioelectrical impedance 

analysis accurately estimate 

the condition of threatened 

and endangered desert fish 

species? Transactions of the 

American Fisheries Society

2017

Journal 

Article

M.C. Dzul, C.B. Yackulic, J. 

Korman, M.D. Yard, and J.D. 

Muehlbauer (2016) 

Incorporating temporal 

heterogeneity in environmental 

conditions into a somatic 

growth model. Canadian 

2016
54

Journal of Fisheries and 

Aquatic Sciences. DOI: 

10.1139/cjfas-2016-0056. 

Online

Journal 

article

MC Dzul, CB Yackulic, DM 

Stone, DR Van Haverbeke 

(2016) Survival, growth, and 

movement of subadult 

humpback chub, Gila cypha, in 

the Little Colorado River, 

Arizona. River Research and 

Applications. 32: 373–382.

2016

Journal 

article 

C Finch, Pine WE, Yackulic 

CB, Dodrill MJ, Yard M, 

Gerig BS, Coggins LG, and 

Korman J (2016) Assessing 

Juvenile Native Fish 

Demographic Responses to a 

Steady Flow Experiment in a 

Large Regulated River. River 

Research and Applications.

32: 763–775

2016

Journal 

article

DL Ward, and R MortonStarner (2015) Effects of water 

temperature and fish size on 

predation vulnerability of 

juvenile humpback chub to 

rainbow and brown trout.

Transactions of the 

American Fisheries Society 

144(6) 1184-1191.

2015

Journal 

article

MJ Dodrill, CB Yackulic, B 

Gerig, WE Pine, J Korman and 

C Finch (2015) Do 

management actions to restore 

rare habitat benefit native fish 

conservation? Distribution of 

juvenile native fish among 

shoreline habitats of the 

Colorado River. River 

Research and Applications. 

31: 1203–1217

2015

Professiona

l Report

Runge, M.C., LaGory, K.E., 

Russell, K., Balsom, J.R., 

Butler, R.A., Coggins, J.L.G., 

2015
55

Grantz, K.A., Hayse, J., 

Hlohowskyj, I., Korman, J., 

May, J.E., O'Rourke, D.J., 

Poch, L.A., Prairie, J.R., 

VanKuiken, J.C., Van 

Lonkhuyzen, R.A., Varyu, 

D.R., Verhaaren, B.T., 

Veselka, T.D., Williams, N.T., 

Wuthrich, K.K., Yackulic, 

C.B., Billerbeck, R.P. & 

Knowles, G.W. (2015) 

Decision analysis to support 

development of the Glen 

Canyon Dam long-term 

experimental and management 

plan. Scientific Investigations 

Report, pp. 80. Reston, VA.

Conference 

Presentatio

n

DL Ward, B. Vaage, K. 

Sheehan, and C. Nelson 

(2016). Effects of elevated 

Carbon Dioxide on fish 

populations within the Little 

Colorado River in Grand 

Canyon. 48th Annual Meeting 

of the Desert Fishes Council, 

Nov 15-19, 2016, 

Albuquerque, NM.

Nov. 2016

Conference 

presentatio

n

CB Yackulic (2016) 

Determining the relative roles 

of environmental drivers and 

competition in the population 

dynamics of Rainbow Trout 

and Humpback Chub to inform 

management of Glen Canyon 

Dam. World Congress on 

Natural Resource Modelling. 

Flagstaff, Arizona. 

July 2016

Invited 

Seminar

CB Yackulic (2016) Managing 

for endangered species in 

novel ecosystems. Cary 

Institute of Ecosystem Studies. 

Millbrook, New York.

March 

2016
56

Conference 

presentatio

n

CB Yackulic (2015) 

Population dynamics of 

Humpback Chub that spawn in 

the Little Colorado River: 

drivers and their implications 

for management. Biennial 

Conference on Science and 

Management on the 

Colorado Plateau. Flagstaff, 

AZ. 

Oct. 2015

Conference 

presentatio

n

MC Dzul, and CB Yackulic 

(2015) Using environmental 

covariates to predict growth in 

two contrasting environments: 

a growth assessment of an 

endangered desert fish.

Biennial Conference on 

Science and Management on 

the Colorado Plateau. 

Flagstaff, AZ.

Oct. 2015

Conference 

presentatio

n

JD Muehlbauer, TA Kennedy, 

EW Kortenhoeven, JT Smith 

(2015) Longitudinal and 

temporal patterns of food 

availability for endangered 

humpback chub, Gila cypha, in 

the Little Colorado River, 

Arizona. Desert Fishes 

Council Annual Meeting, 

Death Valley, NV.

Nov. 2015
57

Project 7 Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $603,400 $13,300 $52,400 $555,000 $0 $96,828 $1,320,928

Actual

Spent $538,288 $12,170 $133,160 $452,093 $0 $95,481 $1,231,193

(Over)/Under

Budget $65,112 $1,130 ($80,760) $102,907 $0 $1,347 $89,735 

FY15 

Carryover $102,781 CPI Decrease ($66,877) FY16 Carryover $125,639 

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Salary costs decreased due to vacancies and some employees working on non-AMP projects.

- Operating expenses increased due to sending funds to a university through a research work order vs. a 

cooperative agreement and purchasing field equipment.

- Cooperative agreements decreased due to sending funds to a university through a research work order vs. a 

cooperative agreement.

- Carryover will be used to maintain employees and to offset FY17 shortage.
58

FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 8: Experimental Actions to Increase Abundance and Distribution of Native Fishes in Grand 

Canyon

Program Manager 

(PM) David Ward Principal Investigator(s) (PI)

David Ward, USGS, GCMRC

Brian Healy, NPS

Clay Nelson, NPS

Emily Omana, NPS

Kirk Young, USFWS

Dennis Stone, USFWS

Randy VanHaverbeke, USFWS

David Rogowski, AZGFD

Scott VanderKooi, USGS, 

GCMRC

Email dlward@usgs.gov

Telephone (928) 556-7280

SUMMARY

This project encompasses two ongoing management actions, a protocol evaluation panel review and two new 

projects funded in 2017. The protocol evaluation panel took place in August of 2016. Specific findings from 

the funded monitoring and research projects are listed below.

Project Element 8.1. Efficacy and Ecological Impacts of Trout Removal at Bright Angel Creek

Goals and Objectives: The objective of this project is to evaluate the feasibility and efficacy of brown trout 

removal in and around Bright Angel Creek using electrofishing, and assess the response of native fish to 

brown trout removal. This experimental action is being conducted in collaboration with Grand Canyon 

National Park, consistent with the National Park Service (NPS) Comprehensive Fisheries Management Plan 

and related compliance documents. 

Summary of progress: Trout removal using boat mounted electrofishing has occurred in the mainstem 

Colorado River near the confluence with Bright Angel Creek annually since 2013–2014, with a trip scheduled 

for January 29 – Feb 5, 2017 (Table 1). 

Summary of trends: Bright Angel Creek inflow removal efforts have varied in scope and intensity from year 

to year, making direct comparisons of trout captures difficult. In 2013–2014, 5 depletion passes were 

conducted over approximately 9 km (Zoroaster to Horn Creek). In 2015–2016, 10 depletion efforts were 

focused on the 4-km section from Bright Angel Creek inflow to Horn Creek (where th majority of fish were 

captured during the previous year’s sampling). In 2016-2017, efforts were further reduced to 5 depletion 

passes between Bright Angel Creek inflow to Horn Creek. Turbid conditions were present for the majority of 

each sampling effort.

Trout catches decreased from 1,709 trout in 2013–2014 to only 25 trout in 2015–2016. In contrast, native fish 

catches increased over this same period, with 294 native fish captured in 2015–2016 up from 132 in 2013–

2014 (Table 1). The apparent decrease in trout abundance near the Bright Angel Creek confluence also 

coincides with decreases in trout observed throughout Glen and Marble Canyons and a significant reduction 

of trout within Bright Angel Creek. This reduction also corresponds to poor condition observed in rainbow 

trout in our study area as well as throughout the system since 2014 (see Project 6 and 9 reports). Increases in 

the catch of native species are likely due to a combination of increased sampling in 2015 compared to 2014 (5 

to 10 depletions), and sampling effort occurring later in the spring when flannelmouth sucker spawn in Bright 

Angel Creek. These changes may also represent increased native fish abundance as a result of ongoing 
59

nonnative fish removals by this project and the NPS in Bright Angel Creek. A system-wide decline in trout 

abundance related to poor condition could also be a factor. 

Table 1. Catch summaries for each species by trip (BNT = Brown Trout, RBT = Rainbow Trout, FMS = Flannelmouth Sucker, BHS = Bluehead 

Sucker, HBC = Humpback Chub, SPD = Speckled Dace, CRP + Common Carp, BBH = Black Bullhead, PKF = Plains Killifish, FHM = Fathead 

Minnow)

Trip BN

T

RBT FMS BHS HBC SPD CRP BBH PKF FHM

2013-

2014

332 1377 90 40 1 1 18 1 1 1

2014-

2015

84 391 270 120 0 0 8 0 0 0

2015-

2016

9 16 204 88 2 0 5 0 0 0

2016-

2017

Sampling scheduled for January 29th to February 5th, 2017

Project Element 8.2. Translocation and monitoring of Humpback chub above Chute Falls in the Little 

Colorado River

The goals of this project are to:

1) Annually translocate at least 300 juvenile humpback chub from lower portions of the Little Colorado 

River (LCR) to above Chute Falls in the LCR. 

2) Annually monitor the abundance of humpback chub above river kilometer (rkm) 13.6 km in the LCR. 

This includes monitoring in a small reach of river known as the Atomizer reach (rkm 13.6–14.1) and 

the reach of river known as the Chute Falls reach (rkm 14.1 km–17.7).

This project is a direct attempt to conduct a conservation measure to translocate humpback chub to upstream 

of rkm 13.6 in the Little Colorado River (LCR) (USFWS 2008, 2011), and is intended to increase growth 

rates and survivorship, expand the range, and ultimately augment the LCR humpback chub aggregation in 

Grand Canyon. In addition, this project provides managers with an annual index of abundance and trend of 

humpback chub residing above rkm 13.6. 

Translocation:

Efforts to translocate humpback chub upstream of Chute 

Falls in the LCR have been ongoing since 2003. To date, 

approximately 3,106 juvenile (~80-130 mm TL) 

humpback chub have been translocated upstream of Chute 

Falls (Figure 1). Of these, 137 humpback chub were 

released above Chute Falls (at rkm 16.2) on October 27, 

2016. The project is identified as a Conservation Measure 

in the 2011 Biological Opinion. Our monitoring activities 

also coincide with joint efforts with the NPS to collect 

juvenile or larval humpback chub for transport to the 
60

Southwest Native Aquatic Research and Recovery Center (SNARRC), destined for grow out and release into 

Shinumo and Havasu Creeks. 

Monitoring:

From 2006–2009, two pass mark-recapture population estimates of humpback chub were conducted upstream 

of rkm 13.6 in the Atomizer Falls and Chute Falls reaches of the LCR. During these trips, capture probability 

data was obtained. From 2010–2016, this set of capture probability data was used to annually estimate the 

abundance of humpback chub upstream of rkm 13.6 (Figure 2). During 2016, a trip was conducted during 17-

25 May to estimate abundances of humpback chub upstream of rkm 13.6 in the LCR. We estimated there 

were 319 humpback chub ≥100 mm (SE = 71) in the Chute Falls reach, and 475 ≥100 mm (SE = 88) in the 

Atomizer Falls reach. Of these, it was estimated that there were 118 humpback chub ≥200 mm (SE = 22) in 

the Chute Falls reach, and 331 ≥200 mm in the Atomizer reach (SE = 57). Results have also indicated 

unusually rapid growth of translocated fish, and high apparent survival. 

Figure 1. Numbers of humpback chub that have been translocated upstream of Chute Falls since 2003 (black bars), and estimated abundances (±95% 

CI) of adult humpback chub (≥ 200 mm) in upper reach upstream of Chute Falls (river km [rkm] 14.1 to 17.7).

Figure 2. Abundances (±95% CI) of adult humpback chub in lower reach downstream of Chute Falls (rkm 13.6 – 14.1) since summer 2006. Note, 

abundances for both above below Chute Falls are shown as those estimated with Chapman Petersen mark-recapture (dark grey bars) and those 

estimated using capture probability data (light grey bars) derived from the 2006-2009 Chapman Petersen mark-recapture efforts.
61

Project Element 8.3.Glen Canyon Dam Adaptive Management 

Program Fisheries Research, Monitoring, and

Management Actions Protocol Evaluation Panel

A Protocol Evaluation Panel was convened in Flagstaff, AZ on August 

2-5, 2016. The Panel members consisted of 5 subject experts, Andrew 

Casper, PhD - Illinois Natural History Survey, Keith Gido, PhD -

Kansas State University, Donald Jackson, PhD - University of Toronto, 

James Petersen, PhD - Oregon State University, Oregon Cooperative 

Fish and Wildlife Unit, and Frank Rahel, PhD - University of Wyoming.

Panelists heard presentations on all aspects of fish monitoring, research, 

and management actions currently being conducted in the Colorado 

River Ecosystem and then participated in discussions with scientists and 

stakeholders at the USGS Science Center in Flagstaff and at Lees Ferry.

The final report with recommendations from the panelists is expected 

this winter.

Project Element 8.4. Little Colorado River Invasive Aquatic Species 

Surveillance

Project element funded in FY17.

Project Element 8.5. Genetic monitoring of Humpback chub in Grand Canyon

Project element funded in FY17.
62

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Trip

Report

Bright Angel Creek inflow trout 

reduction pilot study. Trip Report, 

4-20 February 2015.

Aug

2015

Trip 

Report

Stone, D.M. 2016. Spring 2016 

Monitoring of Humpback Chub 

(Gila cypha) and Other Fishes 

above Lower Atomizer Falls in the 

Little Colorado River, Arizona. Trip 

Report 17-25 May 2016.

July 2016

Trip 

Report

Stone, D.M. and M.J. Pillow. 2016. 

Fall 2016 Monitoring of Humpback 

Chub (Gila cypha) and other Fishes 

in the Lower 13.57 km of the Little 

Colorado River, Arizona. Trip 

Report: 20-30 Sept and 18-28 Oct 

2016. In prep.

Nov

2016

Nov 2016

Annual 

Report 

Van Haverbeke, D.R., K. Young, 

D.M. Stone and M.J. Pillow. In 

prep. Mark recapture and fish 

monitoring activities in the Little 

Colorado River in Grand Canyon 

from 2000 to 2016.

Jan 

2017

Jan 2017

USGS 

Report

2016 Protocol Evaluation Panel 

Review of fish monitoring, research 

and management actions in the 

Colorado River Ecosystem

Jan 2017
63

Project 8 Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $61,400 $0 $5,100 $88,200 $0 $10,615 $165,315 

Actual

Spent $25,465 $180 $3,000 $70,888 $0 $5,559 $105,092 

(Over)/Under

Budget $35,935 ($180) $2,100 $17,312 $0 $5,056 $60,223 

FY15 

Carryover $11,167 CPI Decrease ($8,370) FY16 Carryover $63,020 

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Reduced salary costs due to vacancies.

- Cooperative agreements decreased due to PEP Panel funded from project 15.

- Carryover will be used to offset FY17 shortage.
64

FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 9: Understanding the Factors Determining Recruitment, Population Size, Growth, and 

Movement of Rainbow Trout in Glen and Marble Canyons

Program Manager 

(PM) Mike Yard Investigator(s) (I) Mike Yard, USGS, GCMRCKim Dibble, USGS, GCMRC

Josh Korman, Ecometric 

Research

Charles Yackulic, USGS, 

GCMRC

Ted Melis, USGS, GCMRC

David Rogowski, AZGFD

Ted Kennedy, USGS, GCMRC

David Ward, USGS, GCMRC

Mike Dodrill, USGS, GCMRC

Dan Buscombe, USGS, GCMRC

Paul Grams, USGS, GCMRC

Tom Gushue, USGS, GCMRC

Email myard@usgs.gov

Telephone (928) 556-7377

SUMMARY

Project Element 9.1. Rainbow Trout Population Dynamics – Ongoing Modelling and Future 

Monitoring

In 2016, GCMRC in conjunction with the Science Advisors program convened a protocol evaluation panel 

(PEP; see Project Element 8.3) to review the fisheries monitoring program. Multiple cooperators AGFD 

(Project Element 6.8) and Ecometric (Project Element 9.2), USFWS (Project Element 7.3), and GCMRC 

presented data and provided expert opinion on the long-term status and trend information for native and 

nonnative species. All of these fishery data, technical reports, and scientific papers were evaluated to 

determine whether or not conventional catch-per-unit indices or other types of sampling approaches were 

appropriate for meeting long-term monitoring needs of the GCDAMP. The development of this fisheries 

monitoring plan is a collaborative process that involves current cooperators (USFWS, NPS, AGFD, and 

Ecometric, Inc.). Upon final review, PEP recommendations are to be incorporated into the new monitoring 

project and implemented in FY17. The PEP report is to be finalized by December 2016.

Project Element 9.2. Detection of Rainbow Trout Movement from the Upper Reaches of the Colorado 

River below Glen Canyon Dam/Natal Origins 

Identifying the factors that control the abundance and movement of rainbow trout near the Little Colorado 

River (LCR), and effects of trout on humpback chub, are considered one of the more critical information 

needs of the Glen Canyon Dam Adaptive Management program (GCDAMP). The Natal Origins (NO) project 

was designed to better understand rainbow trout population dynamics by evaluating linkages between 

populations in the Lees Ferry reach and other downstream reaches in Marble and Eastern Grand Canyons (Fig 

1). Toward that goal, alternative sampling and analytical methods were developed for estimating abundance, 

survival, recruitment and capture probability. The primary research objectives are to quantify the extent of 

trout movement from Lees Ferry into Marble Canyon and the LCR confluence area. And to determine the 

physical and biological factors responsible for trout movement (density, food, growth, turbidity, high flow 

experiments (HFEs), etc.).
65

Stakeholders in the GCDAMP often ask specific questions 

about the effects of a variety of flows on biological 

resources, and whether or not current monitoring programs 

are capable of addressing these questions. For that reason, 

the NO project used estimates of rainbow trout capture 

probability from a global open population model for Lees 

Ferry, which does not include density dependent effects, 

and estimates of capture probability from a density 

dependent model, to back calculate abundance of rainbow 

trout in the Glen Canyon tailwater using AGFD’s historic 

time series of boat electrofishing catch-per-unit-effort 

(CPUE). The main objective of this analysis is to determine 

if the effects of fish size and density on capture probability 

result in different long-term trends in abundance relative to 

the trend based on the uncorrected CPUE time series. The 

results determined that surveys based on a CPUE index 

have utility for monitoring long-term trends in abundance, 

but may be too imprecise and potentially biased to evaluate 

population response to flow and habitat changes over 

shorter time scales. Failure to account for effects of fish 

density on catchability in the uncorrected CPUE index led 

to a 3-fold underestimate in the maximum extent of 

variation in abundance over the period of record, and resulted in unreliable estimates of relative change in 

critical years (Fig 2). Essentially, the CPUE index overestimated the relative abundance when actual 

abundance was very low, and underestimated relative abundance when actual abundance was very high. 

These results suggest that stronger inferences can be extracted from sporadically delivered flow treatments or 

naturally occurring events if they are assessed using mark-recapture- rather than CPUE-based surveys.

Figure 1 Map of the study area showing the location of the five 

reaches sampled: I) Lees Ferry, II) House Rock, III) Buckfarm, 

IVa) upstream of the Little Colorado River, and IVb) downstream 

of the Little Colorado River. Numbers beside the mainstem 

Colorado River denote river kilometers downstream of Glen 

Canyon Dam.
66

Figure 2. Comparison of estimated rainbow trout abundance (total of all size classes, N) trends and the Catch per Effort (CpE) trend in Glen Canyon. 

For predicted abundance values, points represent the mean of posterior distributions and vertical lines denote 80% credible intervals. Estimated 

abundance is based on expanding CpE by size-stratified capture probability estimates or by capture probabilities determined by the density-dependent 

relationship. 

In FY16, the NO project completed the last of its four scheduled downstream river trips (Jan, Apr, Jul, and 

Sep 2016, 21-day trips) and including three fall-Lees Ferry trips (Oct and Dec 2015, & Oct 2016, 10-day 

trips). Trout densities throughout all the study reaches continues to remain low relative to the initial density 

estimates made across reaches in 2012 (Fig 3). But unlike previous year’s (2013-2014), trout growth and 

condition are higher and remain elevated across multiple seasons, particularly during the late-summer and 

fall. As previously reported, reduced growth in 2014 occurred when trout biomass was relatively low 

compared to the start of the study, indicating that availability of prey had declined. Reduced growth affected 

multiple life history stages and processes, all potentially causing negative feedbacks that would regulate the 

abundance and biomass of the trout population, including: higher mortality of larger fish; lower rates of 

recruitment in years when growth was reduced; and lower rates of sexual maturation the following year. 

Additionally, NO project results show that inter annual variation in survival rates of post-recruit life stages 

can have very substantive effects on population trends. We estimated that the abundance of rainbow trout in 

Glen Canyon declined by 10-fold over the five-year study period. Although trout abundance levels have been 

reduced across all of the reaches sampled (see Fig. 1), the remaining rainbow trout appear to have recovered 

and are demonstrating better seasonal growth and condition. In Lees Ferry, elevated growth throughout the 

fall of 2015 and winter of 2016 led to excellent reproductive condition for the remaining adult fish. Although 

the total number of potential spawners in 2016 was limited due to lower abundance levels their reproductive 

success was higher than in past years (with the exception of the 2011 cohort) resulting in higher densities of 

age-0 fish (Fig 3). Increased growth rates and likely survival culminated into a very strong year class that is 

recruiting into the adult population, and outcome that will likely increase the abundance of catchable sized 

fish in the Lees Ferry trout population over the next few years. 

Year

19911992199319941995199619971998199920002001200220032004200520062007200820092010

0

0.2

0.4

0.6

0.8

1

0

0.1

0.2

0.3

0.4

0.5

Abundance in Glen Canyon (mCpE (per m)

N (density independent)

N (density dependent)

CpE
67

Figure 3. Estimated abundance of rainbow trout by 50 mm size class by reach (see Fig. 1 for reach locations) and trips. 

Over the past 5 years, the NO study has reported on trout movement from Lees Ferry into Marble Canyon and 

the LCR confluence area. Earlier results indicate that there was limited outmigration of rainbow trout from 

Lees Ferry into Marble Canyon, with the exception of the 2011 age-0 cohort that likely moved prior to the 

start of the study (based on larger taggable sized fish [≥ 75 mm fork length]). Recapture information for 

across-reach movement percentages indicate very limited movement between most reaches. And on average 

only 1% of tagged trout in reaches I, II, or III were estimated to move between reaches other than the ones 

they were released in. The analyses and inferences were based on recapture data that showed there was a 

higher probability of trout moving from locations in Marble Canyon to the LCR, rather than directly from 

Lees Ferry to the LCR. Although the proportion of fish emigrating from upstream reaches down to the LCR 

was very small, all of the recruitment into reaches near the LCR that drove the increasing trout population 

trend can be explained by immigration from the upstream sources in Marble Canyon. Similarly, abundance 

estimates for reaches I, II, and III showed declining trends in trout abundance due to limited recruitment from 

either trout movement or local reproduction. In contrast, downstream reaches (IVa and IVb) demonstrated 

gradual increases in trout density that can be explained entirely by estimated immigration into the lower 

reaches. Initially, the upstream populations were large and therefore provided enough immigration to increase 

the abundance of the relatively small population of trout residing upstream and downstream of the LCR. By 

2015, following the system-wide decline and collapse of trout across all study reaches there was inadequate 

downstream movement from upstream sources to maintain higher densities in reaches IVa and IVb. 

On the July 2016 trip, age-0 trout (< 125 mm FL) made up 25%, 7%, and 1% of the total electrofishing catch 

in reaches I, II, and III, respectively. In comparison, the percentages of age-0 trout that comprised the total 

electrofishing catch on the September 2016 trip increased to 62%, 78%, and 64% in reaches I, II, and III, 

respectively. It is quite likely that age-0 trout emigrated out of Lees Ferry into the upper Marble Canyon 

I

0

5

10

15

20

25

30

35

Apr2012Jul2012Sep2012Jan2013Apr2013Jul2013Sep2013Jan2014Apr2014Jul2014Sep2014Jan2015Apr2015Jul2015Sep2015Jan2016Apr2016Jul2016Sep2016

II

0

5

10

15

20

Apr2012Jul2012Sep2012Jan2013Apr2013Jul2013Sep2013Jan2014Apr2014Jul2014Sep2014Jan2015Apr2015Jul2015Sep2015Jan2016Apr2016Jul2016Sep2016

III

0

1

2

3

4

5

Apr2012Jul2012Sep2012Jan2013Apr2013Jul2013Sep2013Jan2014Apr2014Jul2014Sep2014Jan2015Apr2015Jul2015Sep2015Jan2016Apr2016Jul2016Sep2016

IVA

0.0

0.5

1.0

1.5

2.0

Apr2012Jul2012Sep2012Jan2013Apr2013Jul2013Sep2013Jan2014Apr2014Jul2014Sep2014Jan2015Apr2015

Jul2015Sep2015Jan2016Apr2016Jul2016Sep2016

IVB

0.0

0.5

1.0

1.5

Apr2012Jul2012Sep2012Jan2013Apr2013Jul2013Sep2013Jan2014Apr2014Jul2014Sep2014Jan2015Apr2015Jul2015Sep2015Jan2016Apr2016Jul2016Sep2016

Size Class (mm)

300

250

200

150

100

Abundance ('000s per km)
68

section sometime between July and September 2016. Reach comparisons of length frequency distributions for 

age-0 fish were all similar in size among all reaches. This represents a paradox, as there is no past evidence of 

local reproduction in reach II over the study period, and only limited local reproduction in reach III. Also, 

over 60% of age-0 fish remained well below the passive integrated transponder (PIT) taggable size. Most of 

the downstream movement from Lees Ferry appears to be episodic with the majority of emigration due to 

large recruitment events (2011 and 2016) of age-0 fish into upper Marble Canyon, or secondarily from longdistance movement of larger fish (e.g., April and September 2014). The long-distance movement of larger 

trout into the LCR region was likely in response to poor growth and reduced survival, a response similarly 

reported by Coggins et al. (2011) where net immigration rates were elevated during 2003–2004. These same 

years also corresponded to periods when the overall trout population declined system-wide.

A system-wide increase of trout followed by a rapid decline is characteristic of a boom-bust cycle. The recent 

decline in trout (2012-2016) would be novel if not for other boom and bust cycles that have previously 

occurred in the Glen Canyon trout population (1989-1992 and 2002-2006) (Arizona Game and Fish Dept., 

unpublished data; Makinster et al. 2010). When we reevaluated AGFD’s historical trend data for the Glen 

Canyon fishery, using a time-series of average annual CPUE, it corresponded strongly with the variation in 

average annual surface elevation of Lake Powell and nutrients levels (1990-2015) supplied to the river 

outflow. During the limited period of this study, annual inflows into Lake Powell from the major upstream 

sources of the Green River, Colorado River and San Juan rivers were well below the average annual runoff 

level, which resulted in a drawdown of the reservoir volume. Historically, the total annual inflow from the 

three riverine sources (flow record, 1984-2015) has ranged from a maximum volume of 21,107 million cubic 

meters (MCM) to a low of 510.6 MCM. Since the post filling period (1963-1980), the reservoir volume has 

varied annually and corresponds in time with three periods of declining trout CPUE, and two periods of 

increasing CPUE. Reservoir limnology and inflow hydrology govern the quantity of nutrients that are 

supplied to the downstream river segments of Glen and Grand canyons. Phosphorous levels are critical for 

aquatic primary production, but in this system phosphorous levels are often measured at or below detectable 

levels (25% of WQ period of record). Some invertebrates, specifically Gammarus and certain species of 

Chironomids utilize primary producers like algae as refuge and for food resources. Preliminary results based 

on trout bioenergetic demand (daily prey intake) (Fig 4), and invertebrate drift availability would indicate that 

annual production of invertebrate prey declined over the NO study interval (2012-2016). Our inference on 

causation is weak and needs to be strengthened or falsified with better experimental designs and 

manipulations that address specific hypotheses a-priori rather than a reliance on retrospective analysis of 

CPUE trends.
69

Figure 4. Total daily prey intake by rainbow trout estimated for the six size classes (125-174 mm, 175-224 mm, 225-274 mm, 275-324 mm, ≥ 325 

mm) over the study period (2012-2015). Estimates of invertebrate prey consumed per day are expressed in units of weight (Kg of ash free dry mass 

[AFDM] per day).

Our analysis indicates that there can be considerable inter-annual variation in prey supply for trout, and that 

this supply will not always be sufficient to sustain the trout population. Our hypothesis is that reduced 

invertebrate production in 2014 was driven by lower concentrations of nutrients in the water released from 

Glen Canyon Dam. Increasing prey production is an obvious way to avoid future collapses, but factors that 

likely control it, such as reservoir inflow and elevation, are largely determined by climate variation and 

cannot be controlled by managers. Thus, limiting trout recruitment (age-0), or at least avoiding very large 

recruitment events, is a more viable strategy to avoid future collapses. Owing to these findings, GCMRC 

considers it warranted to reexamine and further improve on the current water quality program, particularly the 

sampling frequency and precision of analyses used. Future work plans (FY18-20) should place greater 

emphasis on studying nutrient limitations, since phosphorous is an essential limiting nutrient in most aquatic 

ecosystems, particularly those that rely heavily on photosynthesis to support higher trophic levels. 

Additionally, we propose to maintain a mark-recapture program focused in Glen Canyon to determine effects 

from HFEs and potential trout management flows (TMF) that cannot be adequately addressed solely by 

CPUE based monitoring programs.

Two papers have recently been submitted for publication (entitled “Trends in recruitment, abundance, 

survival, and growth over a boom-and-bust cycle of a rainbow trout tailwater population.”, and “On the 

Catchability of Fish Populations and Interpretation of Catch per unit effort Trends”), and a third manuscript 

on prey consumption and bioenergetic demand is in progress (entitled “Invertebrate production estimates 

from bioenergetic demand by rainbow trout in the Colorado River in Grand Canyon”).

Project Element 9.3. Exploring the Mechanisms behind Trout Growth, Reproduction, and Movement 

in Glen and Marble Canyon using Lipid (fat) Reserves as an Indicator of Physiological Condition 

The purpose of this project was to determine whether the ability of adult trout to acquire and store energy 

from the prey base is a potential mechanism behind spatial and temporal differences in growth, reproduction, 

and movement of rainbow and brown trout in Glen and Marble Canyons. Field data collection was completed 

in FY15 during fish sampling associated with the Natal Origins Project (9.2). Approximately 100 rainbow 

0

10

20

30

40

50

60

70

Dec-11 Jun-12 Dec-12 Jun-13 Dec-13 Jun-14 Dec-14 Jun-15 Dec-15

Prey Intake (Kg AFDM da-1)

125-174

175-224

225-274

275-324

>325
70

trout and 25 brown trout were sampled during each trip and muscle, liver, and hindgut tissue excised in the 

field. 

In FY16 we analyzed all samples these were processed in the laboratory and lipids were extracted from each 

tissue sampled using gravimetric extraction techniques. At the present time, data acquisition and a preliminary 

analysis is complete. A more in-depth analysis that includes information from the food base (e.g., stomach 

contents, drift) as well as other biological and physical factors is planned this winter, and one manuscript 

associated with Project 9.3 will be prepared for submittal to a peer-reviewed journal in FY17. 

Project Element 9.4. Comparative study on the feeding morphology of drift feeding fish (NOT 

FUNDED) 

This project element was not funded.

Project Element 9.5. Meta-analysis, and the development of reactive distance relationships for 

encounter rate model.

The objective of this project element contains two parts: (1) determine the effects of varying light intensity 

and prey size on fish reactive distances; and (2) develop an encounter rate model for drift feeding fish that 

accounts for varying reactive distances and prey availability within the range of channel depths and light 

levels encountered in Glen and Marble Canyons. An extensive literature search on all known published data 

on reactive distances (i.e., distance a prey item can be visually detected) of visual sight-feeding fish was 

performed. We will evaluate literature and quantitatively summarize regression slopes obtained from 

independent studies, either published as relationships or through extraction of data from graphs and tables.

We are currently analyzing the data and are preparing to develop a manuscript associated with these results in 

2017. The paper will be submitted to a peer-reviewed journal at the end of FY17.

Project Element 9.6. Evaluation of Turbidity (in terms of TSS) as a potential Glen Canyon Dam 

operations management tool to constrain rainbow trout populations and reduce predation/competition 

on juvenile humpback chub 

The objective of this project is to determine what level and duration of turbidity might be necessary to 

negatively effect, or prevent persistence of, rainbow trout in lower Marble Canyon and to determine whether 

turbidity levels in the mainstem Colorado River could be manipulated so as to limit rainbow trout survival 

downstream of the Paria River.

We have constructed 4 recirculating artificial stream systems at the US Forest Service Rocky Mountain 

Research Station in Flagstaff, Arizona. These stream systems are capable of maintaining turbidities of 50 –

200 formazin nephelometric units (FNU) in suspension without deterioration in water quality. PIT-tagged 

rainbow trout were collected from Lees Ferry, acclimated to laboratory conditions, and placed into the 

laboratory apparatus with abundant live feed. Two streams were maintained at low turbidities of 50 -100 FNU 

and two streams held clear water. To date, we have only completed a single replicated trial with adult rainbow 

trout, but additional trials will take place this winter and spring. Rainbow trout from the turbid tanks gained 

an average of 9.6 grams over the 30-day trial while trout from the turbid tanks lost an average of 23 grams 

over the same time period (Fig. 5). From a laboratory experimental perspective, it does appear that relatively 

low levels of turbidity (<100 FNU) could be used as a management tool to disadvantage trout in as little as 30 

days, although additional replicates and sizes of fish need to be evaluated. Evaluations of historic turbidity 

levels below the confluence of the Paria River and potential links to fluctuations in trout populations and trout 

condition are currently being examined.
71

Figure 5. Effects of low level turbidity (<50 FNU) on rainbow trout as measured by mean change in weight during a 30-day laboratory trial. Error bars 

indicate 95% confidence intervals around the mean change in weight.

Project Element 9.7. Application of a bioenergetics model in a seasonally turbid river 

Prior drift-foraging bioenergetics approaches applied to rainbow trout at Lees Ferry have elucidated the 

importance of invertebrate prey to trout growth. This project element looks to expand this work and explore 

how other factors including turbidity influence conditions for rainbow trout growth. We continue to refine 

these process-oriented models in order to improve our ability to predict how trout may respond to changing 

physical and biological conditions. We have advanced these modeling approaches by identifying important 

biases that drift-foraging models have in relation to model structure and input (Dodrill and Yackulic 2016). 

Additionally, we have used information collected during Natal Origins (Project 9.2) trips on invertebrate drift 

rates (Project Element 5.2.2) and rainbow trout diets to assess prey selectivity of rainbow and brown trout. 

This is accomplished using a discrete choice model, fit within a Bayesian modeling framework. The modeling 

approach allows us to quantify factors influencing prey selection, including prey size, identity, and how prey 

selection changes in response to turbidity. 

These finding are reported in a manuscript in preparation (Dodrill et al. In Prep) which is to be submitted to 

Canadian Journal of Fisheries and Aquatic Sciences. Knowledge of prey selection patterns in relation to 

turbidity can then be incorporated into drift-foraging bioenergetics approaches. This information will help 

guide the application of process based models to understand the role of turbidity in influencing rainbow trout 

foraging and growth.

Project Element 9.8. Mechanisms that Limit Rainbow and Brown Trout Growth in other Western 

Tailwater Systems 

The purpose of this project was to continue to develop a broader understanding of the links between dam 

operations and rainbow and brown trout population dynamics by synthesizing data from tailwaters across the 

western United States. We published the results of our first tailwater synthesis project in FY15 (funded in the 

FY13-14 work plan), which examined the influence of physical and biological variables on rainbow and 

brown trout recruitment and adult size in tailwaters across the western U.S. However, due to limited data we 

could not evaluate the potential influence of water temperature on trout population dynamics. Ongoing 

drought in the region has led to highly-publicized reductions in reservoir storage and raised concerns about 

potential reductions in minimum flows, which may result in large changes in thermal regimes as reservoir 
72

storage drops. Therefore, in FY16 we built on the body of knowledge gained from our first synthesis in two 

ways. First, we added water temperature data to models using a subset of tailwaters included in the first 

synthesis to better understand how temperature influences trout population dynamics and how populations 

may respond to future drought and warming conditions. We analyzed data both within and among ten large 

western U.S. tailwaters and found that water temperature was inversely related to reservoir capacity, such that 

water temperatures increased when reservoir levels dropped. Consequently, rainbow trout recruitment 

increased in years and in tailwaters exhibiting higher temperatures, but adult rainbow and brown trout size 

decreased with higher temperatures. These results suggest that drought-induced temperature increases in 

western U.S. tailwaters will enhance trout recruitment at the expense of adult size. A publication associated 

with these results entitled “Drought induced warming in tailwaters of the Western U.S. increases trout 

recruitment at the expense of maximum size” is currently under review at Canadian Journal of Fisheries and 

Aquatic Sciences. 

Second, we used water temperature, air temperature, and reservoir storage data from the past three decades in 

the Colorado River Basin and from other western tailwaters to quantify how past climate shifts (from drought 

conditions to large precipitation events) influence water temperatures downriver of a variety of dam types 

throughout the intermountain West. Specifically, we examined how different types of dams may nonlinearly 

influence the magnitude and seasonality of tailwater temperatures, which has important implications for 

managing trout populations and maintaining endangered fish populations in a changing climate. We found 

that water temperatures downriver of shallow or run-of-the-river dams are already close to equilibrium with 

air temperatures, so decreases in reservoir size resulting from drought may not substantially influence 

tailwater fisheries in those systems. However, penstocks from large storage dams such as Glen Canyon Dam 

are likely to draw water from closer to the reservoir surface during a drought, substantially increasing 

tailwater temperatures downstream that may benefit endangered fish populations. 

We are currently preparing a manuscript associated with these results entitled “Warmer and drier: predicting 

future thermal regimes in regulated rivers based on past drought conditions” which will be submitted to a 

peer-reviewed journal in FY17.

Project Element 9.9. Effects of High Experimental Flows on Rainbow Trout Population Dynamics 

This information has management implications, particularly below Glen Canyon Dam where rainbow trout 

dynamics are central to understanding how to manage a functional sport fishery at Lees Ferry and its 

downstream relationship to native fish conservation in Grand Canyon. The primary objective of this project is 

to assess the effectiveness of GCDAMP policy actions that directly influence rainbow trout abundance, 

survival, recruitment, and movement in response to HFEs. An experimental comparison of pre- and postflood responses are appropriate for assessing hydraulic effects to biota, but only partly addresses the fluvial 

mechanism that underlie this policy action (refer to Project 10, using an inter disciplinarian approach to 

determine HFE effects). Preliminary results suggests that there might have been a HFE effect on monthly 

growth rates of rainbow trout, particularly when we compare seasonal growth differences based on weight 

change (Fig. 6, shows changes in estimated monthly growth rate for a 200 mm trout across three seasonal 

growing periods). We observed slightly negative trout growth during two of the three fall intervals that span 

the same time period when a HFE was conducted. Secondly, we have observed positive growth during the fall 

of 2015, a year when a HFE was not conducted. Unfortunately, we are uncertain whether or not the observed 

growth differences can be partly or entirely ascribed to a hydraulic effect related to HFEs. Based on trout 

recaptures there is no indication that fish moved or were displaced by any of these HFEs. If there was a flow 

effect it likely acted on the benthic invertebrate community; and secondarily, on trout by reducing the 

invertebrate prey available following the flow disturbance. Unfortunately, the cause and effect relationship 

between the 2014 HFE and trout growth is confounded by what appears to be a much larger effect that was 
73

also occurring at the same time on the benthic invertebrate community, likely over multiple years (nutrient 

hypothesis). Project 9.2, previously reported that trout growth declined incrementally over each year, 

particularly over most of 2014 (Korman et al. 2016, Yard et al. 2016). However, by the early fall period of 

2014 the remaining trout that survived (Fig. 3) showed elevated growth during the start of fall, the time 

interval just prior to the third HFE. This is an interesting response since the fall season is typically less 

productive because of reduced primary production and increased demand for prey due to elevated fall 

temperatures. Yet it is notable that once trout densities were substantively reduced from their former levels 

(Fig. 3), trout growth increased. Was this growth response due to the overall reduction in trout prey demand 

or an actual increase in benthic invertebrates? Nevertheless, this positive trout growth response was brief, 

since we observe a trout growth reduction post-flood. In contrast, the fall period in 2015 showed no reduction 

in trout growth, the only year that lacked a HFE. This same year also had low trout densities and elevated 

invertebrate drift concentrations. Because there are numerous independent factors that are likely confounding 

these results, additional replication is required to determine the causal mechanism for limited trout growth. It 

highlights the importance of making comparisons between pre- and post-flood and between years with and 

without HFEs. Toward that goal, a fish monitoring trip is planned in early January 2017 to determine if there 

was a decrease in trout growth during the fall that included the 2016 HFE.

Figure 6. Trend data for growth of rainbow trout in Lees Ferry (April 2012 to September 2016). The bars show mean monthly growth rates (g/30 days) 

over sampling intervals, estimated for a 200 mm (fork length) rainbow trout, where colors represent seasonal growing periods (yellow = late spring and 

summer, brown = fall, and blue = winter and early spring). 

For more detail on addressing future questions in 2017 related to HFE effects, refer to Project 10.
74

Project Element 9.10. Examining the Effects of High Flow Experiments on the Physiological Condition 

of Age-0 and Adult Rainbow Trout in Glen Canyon 

The purpose of this project is to examine the effects of low, steady fall flows followed by a potentially 

energetically-costly HFEs on the physiological condition of age-0 rainbow trout in Glen Canyon. We 

collected trout from September to December in 2013-2015 to compare pre- and post-flood samples to those 

collected during a control (non-HFE) year. In FY16 we extracted otoliths from post-flood samples, prepared 

them for microstructural analysis, and calculated the daily growth rate of fish associated with various types of 

flows before and after each flood using patterns embedded in otoliths. In addition, we sent pre-flood, postflood, and control fish samples to an independent laboratory to quantify their physiological condition using 

sensitive biochemical indicators (triglyceride, cholesterol, phospholipid, total lipid). These data will be 

compared to food base data collected prior to, during, and after each flood, as well as recruitment data the 

following spring, to determine whether physiology plays a role in the influence of HFE’s on rainbow trout 

population dynamics in Lees Ferry. These data will be analyzed and a manuscript will be submitted to a peerreviewed journal in FY17.

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Journal 

Article

Nonlinear relationships can lead 

to bias in biomass calculations 

and drift-foraging models when 

using summaries of invertebrate 

drift data.

May 2016 Sept 2016

Dodrill, M. J and C. B. 

Yackulic. 2016. 

Environmental Biology of 

Fishes 99.8-9: 659-670. 

Journal 

Article

Prey Selection by Rainbow 

Trout in a Large River 

Ecosystem in Relation to 

Physical and Biological Factors.

July 2017

In prep. Dodrill, M. J., C. 

B. Yackulic, T. A. 

Kennedy and M. D. Yard.

Journal 

Article

Drought induced warming in 

tailwaters of the Western U.S. 

increases trout recruitment at the 

expense of maximum size.

July 2016 Feb 2017

In review. Dibble, K.L., 

C.B. Yackulic, and T.A. 

Kennedy.

Canadian Journal of 

Fisheries and Aquatic 

Sciences

Journal 

Aritcle

Warmer and drier: predicting 

future thermal regimes in 

regulated rivers based on past 

drought conditions.

Feb 2017

In prep. Dibble, K.L., 

C.B. Yackulic, and T.A. 

Kennedy.

Global Change Biology

Journal 

Article

Effects of turbidity on predation 

vulnerability of juvenile 

June 2016

Ward, DL., R. MortonStarner, and B. Vaage.

2016. Journal of fish and 
75

humpback chub to rainbow and 

brown trout.

Wildlife Management 7: 

1-8

Journal 

Article

Effects of water temperature and 

fish size on predation 

vulnerability of juvenile 

humpback chub to rainbow and 

brown trout.

Nov. 2015

DL Ward, and R MortonStarner 2015.

Transactions of the 

American Fisheries 

Society 144(6) 1184-

1191.

Journal 

Article

Factors controlling the 

abundance of rainbow trout in 

the Colorado River in Grand 

Canyon in a reach utilized by 

endangered humpback chub.

Jan. 2016

Korman, J., M.D. Yard, 

and C.B. Yackulic. 

Canadian Journal of 

Fisheries and Aquatic 

Sciences. 73: 105–124

Journal 

Article

Seasonal and Spatial Patterns of 

Growth of Rainbow Trout in the 

Colorado River in Grand Canyon

Jan. 2016

Yard, M.D., J. Korman, 

C. J. Walters, and T.A. 

Kennedy. Canadian 

Journal of Fisheries and 

Aquatic Sciences. 73: 

125–139

Journal 

Article

Trends in recruitment, 

abundance, survival, and growth 

over a boom-and-bust cycle of a 

rainbow trout tailwater 

population.

Nov.

2016

In review. Korman, J., 

and M.D. Yard.

Transactions of the 

American Fisheries 

Society

Journal 

Article

On the Catchability of Fish 

Populations and Interpretation of 

Catch per unit effort Trends

Dec.

2016

In review. Korman, J., 

and M.D. Yard.

Transactions of the 

American Fisheries 

Society

Journal 

Article

Invertebrate production 

estimates from bioenergetic 

demand by rainbow trout in the 

Colorado River in Grand Canyon 

In prep. Yard, M.D., J. 

Korman, C. J. Walters, 

and M.J. Dodrill.

Journal 

Article

Flow management and fish 

density regulate salmonid 

recruitment and adult size in 

tailwaters across western North 

America

Dibble, K.L., C.B. 

Yackulic, T. Kennedy, 

and P. Budy. In Press. 

Ecological Applications.

Presenta

tion

Bioenergetic modeling of Glen 

Canyon rainbow trout fishery—

Exploring effects of temperature, 

trout population size and 

Jan. 2016

Yard, M.D., and J. 

Korman. 2016. GCMRC 

Annual Reporting 

Meeting, Phx. AZ.
76

biomass on the benthic 

invertebrate consumption.

Presenta

tion

Natal Origins of Rainbow Trout 

Project years 1-4 (Nov ’11 – Dec 

‘ 15)

Jan. 2016

Korman, J., and M.D. 

Yard. 2016. GCMRC 

Annual Reporting 

Meeting, Phx. AZ.

Presenta

tion

Boom-and-Bust Cycles in Glen 

Canyon’s Rainbow Trout 

Population

Mar. 2016

Yard, M.D., and J. 

Korman. 2016. Lees 

Ferry Guide Meeting, 

Marble Cyn., AZ

Presenta

tion

Consequences of an altered 

hydrologic regime for Colorado 

River fishes in Grand Canyon

Aug. 2016

Ward, D.L. 2016. 146th 

annual meeting of the 

American Fisheries 

Society, August 21-25, 

2016, Kansas City, MO

Presenta

tion

Drought increases trout 

recruitment at the expense of 

adult size in tailwaters downriver 

of dams in Western North 

America. 

Aug. 2016

Dibble, K.L., C.B. 

Yackulic, and T.A. 

Kennedy. 2016 American 

Fisheries Society Annual 

Meeting. Kansas City, 

MO.

Presenta

tion

The influence of drought and 

climate change on water 

temperature and trout population 

dynamics in Western U.S. 

tailwaters.

Aug. 2016

Dibble, K.L., C.B. 

Yackulic, and T.A. 

Kennedy. 2016.

GCDAMP, Fisheries 

Program Review, 

Protocol Evaluation 

Panel.

Presenta

tion

Using bioenergetics models to 

determine how water 

temperature and food 

consumption influence 

Oncorhynchus mykiss and Salmo 

trutta growth in western U.S. 

tailwaters.

Oct. 2015

Dibble, K.L., C.B. 

Yackulic, and T.A. 

Kennedy. 2016. 13th 

Biennial Conference of 

Science and Management 

on the Colorado Plateau 

and Southwest Region.
77

Project 9 Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $361,200 $5,000 $84,000 $190,000 $0 $59,647 $699,847 

Actual

Spent $350,153 $4,119 $100,675 $140,000 $0 $58,716 $653,663 

(Over)/Under

Budget $11,047 $881 ($16,675) $50,000 $0 $931 $46,184 

FY15 

Carryover $58,249 CPI Decrease ($35,433) FY16 Carryover $69,000 

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Salary costs decreased due to contracting lipid analysis rather than doing in-house.

- Operating expenses increased due to contract for lipid analysis rather than doing in-house.

- Cooperative agreement costs decreased due to reaching funding cap on 5 year agreement with Ecometric.

- Carryover will be used to offset FY17 shortage.
78

FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 10: Where does the Glen Canyon Dam Rainbow Trout Tailwater Fishery End? – Integrating 

Fish and Channel Mapping Data below Glen Canyon Dam

Program Manager 

(PM) Ted Melis Investigator(s) (I) Dan Buscombe, USGS, GCMRC

Mike Yard, USGS, GCMRC

Josh Korman, EcoMetric 

Research

Paul Grams, USGS, GCMRC

Tom Gushue, USGS, GCMRC

Scott, Wright, USGS

Email tmelis@usgs.gov

Telephone (928) 556-7282

SUMMARY

The goal of Project 10 is to promote collaborative efforts between physical and biological scientists using an 

interdisciplinary approach. This project was to help inform resource managers on the Glen Canyon Dam 

Adaptive Management Program (GCDAMP), and in the development of the Long Term Experimental 

Management Plan Environmental Impact Statement (LTEMP) for Glen Canyon Dam operations, and on how 

specific dam operations influence the river’s bed-sediment type, inundation of channel margins used by fish, 

and other aquatic organisms. This information has management implications, particularly between Glen 

Canyon Dam and Lees Ferry where rainbow trout are important as a sport fishery and relative to native fish 

conservation in Grand Canyon. The primary researcher, Ted Melis, Physical Scientist, responsible for leading 

and completing Project 10 has been promoted to Deputy Director of Southwestern Biological Science Center. 

The loss of this key person has potentially jeopardized the successful completion of this project. For this 

reason a revised proposal was submitted that identifies how the stated study objectives and deliverables are to 

be met as specified in the original proposal 

(see: http://www.usbr.gov/uc/rm/amp/amwg/mtgs/14aug27/Attach_06d.pdf). 

The revised proposal is to provide a clear direction and means to meet the stated objectives in Project 10, with 

a focus towards policy related questions. Successful completion of Element 10.3 is largely dependent on the 

continuation of the data collection activities, analysis, and synthesis by original investigators listed in Project 

10, with a slight modification in budget to account for the involvement of two additional cooperators J. 

Korman of Ecometric Research (Vancouver, BC), and Scott Wright, Research Hydrologist, U.S. Geological 

Survey, California Water Science Center.

Project Element 10.1. Imaging channel-bed, bed-texture, and change detection

The purpose of the 10.1 element of this project is to complete sidescan sonar mapping/imaging methods. An 

additional purpose of this project is to finalize a protocol for sidescan data collection. This monitoring 

involves collection and analysis of data, and algorithm development for determining changes in the areal 

extents of sand and gravel bed surface sediment types using low-cost, easy-to-use sidescan sonar technology, 

where drifting benthic organisms and spawning trout are monitored in Glen and Marble Canyon study 

segments.

We have continued refining the methods for sidescan data processing developed in FY2016 and are now 

implementing those methods in an open source software package. That software performs automated 

classifications of bed composition into broad Wentworth-style grouping of sediments (i.e. sand, gravel, 

boulders) by a statistically-based texture analysis [Buscombe in review, Hamill et al. 2016]. We are currently 

processing the data to develop 30-bed classification maps for sidescan sonar surveys collected during 4 
79

sampling trips between April 2014 and April 2015 in the Natal Origins study reach 4a. These data will 

provide objective quantification of riverbed composition at temporal and spatial scales that are consistent with 

fish sampling program.

Project Element 10.2. Analyzing Channel-Margin Geometry, and Shoreline Responses to Flow 

Variation using Channel Map Data

The purpose of this project is to conduct the slope analyses related to proportion of low and high-angle 

channel margins. The geospatial data to be used for processing and analyzing the channel-margin geometry 

and supplying spatial characteristics, such as slope criteria, has been dependent on the development and 

delivery of the channel map digital elevation model (DEM) created and processed under the Geomorphology 

project (Project 3). These data now exist at an acceptable resolution (1-meter) for the Glen Canyon reach, and 

initial tests have been run on how best to merge these data with the airborne digital surface model (DSM) 

elevation collected in May 2013 as part of the remote sensing overflight. Additionally, in order to use the 

airborne data from 2013, elevations in vegetated areas needed to be removed and interpolated so that the two 

merged data sets are both representing bare earth elevations. This task was accomplished in 2016. Once these 

data sets (airborne topography and combined channel map topography) are merged, then a slope map will be 

generated for the entire reach and characterized as low- and high-angle areas. These data will then be 

overlayed with fish sampling unit data as described in Project Element 10.3.

Project Element 10.3. Synthetic Analysis of Rainbow Trout Catch and Physical Data

Purpose of Element 10.3, is to integrate physical (segment-scale channel geometry, changes in areal bed 

surface sand coverage, and variations in flow patterns, total suspended sediment flux and water temperature) 

and biological (the aquatic food base, in terms of invertebrate drift) and rainbow trout responses. Data from 

the first two project elements, Elements 10.1 and 10.2, are on schedule and findings will be available for 

analyses. Other sources of data are to come from Project 9.2, entitled “Detection of Rainbow Trout 

Movement from the Upper Reaches of the Colorado River below Glen Canyon Dam/Natal Origins”, which is 

now available since fieldwork has been concluded (end of FY16). 

Hypotheses being tested include:

1) We hypothesize that sediment supply sources like Honey Draw, Ferry Swale, -9 Mile Draw, 

Waterhole Canyon contribute fines (sands and gravels) to the channel-bed that are available for 

transport and deposition along channel margins during experimental high flows. The spatial 

distribution of fish densities, size-structure, survival, growth, and condition are influenced by these 

cumulative loads, flow fields, and channel margin deposits. Sedimentation is likely to have a greater 

effect on the availability aquatic food resources and by extension indirectly on trout.

2) Higher water velocities during HFEs have the potential to displace trout downstream. We will

compare the location of individually-tagged fish before and after HFEs to evaluate whether 

downstream movement caused by HFE’s is occurring. 

3) HFE’s have the potential to reduce benthic biomass and lower drift densities. If this occurs, rainbow 

trout growth may be reduced following HFE’s. We will compare growth rates before and after HFE’s 

to determine whether this is occurring.

4) Fine sediment loads from tributaries like Ferry Swale and Waterholes Canyon, combined with 

reduced water surface gradient due to downstream controls by effecting the quality of benthic habitat 

for invertebrates which in turn control the growth, condition, and abundance of rainbow trout in Lees 

Ferry.

The available data are to be integrated, analyzed and synthesized into a number of manuscripts and prepared 

for publication by FY17. Topics cover: 1) Direct and indirect effects of high-flow experimental (HFE) on the 
80

rainbow trout fishery, and 2) Spatial patterns in growth, condition, survival, and abundance of rainbow trout 

in Lees Ferry. Lastly, 3) a white paper describing optimal levels for trout management flows. 

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Manu

script

Direct and indirect effects of 

high-flow experimental (HFE) 

on the rainbow trout fishery.

Sep. 

2017

Manu

script

Spatial patterns in growth, 

condition, survival, and 

abundance of rainbow trout in 

Lees Ferry.

Sep. 

2017

Repor

t

Determining optimal levels for 

conducting trout management 

flows.

Sep. 

2017

Hamill, D., Buscombe, D.,

et al., 2016, Towards bed 

texture change detection in 

large rivers from repeat 

imaging using recreational 

grade sidescan sonar. 

Proceedings of the 8th 

International Conference 

on Fluvial Hydraulics, St. 

Louis, Missouri, July 2016.

Buscombe, D., in review, 

PyHum: Python toolbox 

for shallow water physical 

habitat assessment using 

recreational grade sidescan 

sonar. Environmental 

Modeling and Software
81

Project 10 Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

urden

Total

11.983%

Budgeted

Amount $129,800 $5,000 $0 $0 $0 $16,153 $150,953 

Actual

Spent $50,502 $10,000 $0 $25,204 $0 $8,006 $93,712 

(Over)/Under

Budget $79,298 ($5,000) $0 ($25,204) $0 $8,147 $57,241 

FY15 

Carryover ($21,327) CPI Decrease ($7,643) FY16 Carryover $28,271 

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Salary costs decreased due to sending funds to Utah State University for student rather than USGS 

employee.

- Cooperative agreements increased due to sending funds to Utah State University for student rather than 

USGS employee. Also, the cooperative agreement was front loaded so FY17 costs will be lower.

- Carryover will be used to offset FY17 shortage.
82

FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 11: Riparian Vegetation Monitoring and Analysis of Riparian Vegetation, Landform Change 

and Aquatic-Terrestrial Linkages to Faunal Communities

Program Manager 

(PM) Barbara Ralston Investigator(s) (I) Barb Ralston, USGS, GCMRC

Daniel Sarr, USGS, GCMRC

Joel Sankey, USGS, GCMRC

Paul Grams, USGS, GCMRC

Charles Yackulic, USGS, 

GCMRC

Ted Kennedy, USGS, GCMRC

Jeff Muehlbauer, USGS, GCMRC

David Merritt, USFS

Patrick Shafroth, USGS, Fort 

Collins

Joe Hazel, NAU

Emily Palmquist, USGS, 

GCMRC

Laura Durning, NAU

Todd Chaudhry, NPS

Dustin Perkins, NPS

John Spence, NPS

Email bralston@usgs.gov

Telephone (928) 556-7389

SUMMARY

Goals and Objectives FY15–17

Riparian vegetation is an important part of the Colorado River ecosystem in that it influences sediment 

deposition and retention, is key habitat for wildlife, can reduce campable area, adds beauty to the landscape, 

and creates shade and windbreaks. This project aims to monitor changes to riparian vegetation using fieldcollected data and digital imagery (11.1, 11.2), assess possible feedback loops between vegetation and 

sediment on sandbars (11.3), and quantify links among riparian vegetation, terrestrial wildlife, and the aquatic 

ecosystem (11.4). Additionally, this project facilitated a review of success and failures in riparian restoration 

efforts to inform potential restoration in Grand Canyon (11.5).

Project Element 11.1 Ground-based Vegetation Monitoring

Ground-based (field collected data) vegetation monitoring is conducted to quantify changes in cover and 

composition of riparian vegetation. Changes in the amount and kind of vegetation can alter biodiversity, 

affect the interactions with flows and sediment, influence visitor experiences and overall, affect ecosystem 

functioning.

This element of project 11 measures and analyses plant cover and species presence to assess change as related 

to the geomorphic setting, elevation above the channel, and flow regime. The specific objectives of the 

element are:

1. To annually collect vegetation data (presence, cover) within a geomorphic and hydrologic framework 

downstream of Glen Canyon Dam.

2. Use the traits of the plants found to identify plant response-guilds.
83

3. Collect data and describe results in a manner that can 

be utilized by multiple stakeholders, such as for 

monitoring approaches used by Tribal stakeholders and 

for use in basin-wide riparian vegetation monitoring 

programs overseen by the National Park Service’s 

Northern Colorado Plateau Network Inventory and 

Monitoring Program.

Monitoring was conducted August – October in 2015 

and 2016 in both Glen Canyon National Recreation 

Area (GCNRA) and Grand Canyon National Park. In 

2016, data was collected at 89 randomly selected 

sample sites between river mile -15.5 and 240, as well 

as 43 long-term monitoring sites. Both the random site 

and long-term monitoring site data from 2016 are 

currently being entered and error checked. Data from 

2012 – 2015 are available for use. Summaries of the 2014 and 2015 data indicate that vegetation cover 

remained relatively unchanged. Total foliar cover tends 

to be lowest between river miles 61 and 160, but woody 

vegetation cover is fairly constant along the length of 

the study area. While total foliar cover is generally 

higher on channel margins than on debris fans and 

sandbars, woody vegetation is notably higher on 

sandbars in Marble Canyon than in river segments 

downstream of the Little Colorado River. Nonnative 

species cover is highest between river miles 160 to 240, 

likely due to Cynodon dactylon (Bermuda grass). 

Tamarix spp. (Salt Cedar, Tamarisk) is particularly 

high in cover on channel margins in Marble Canyon. A 

species list and summary of the 2016 data will be 

available at the annual reporting meeting in January 

2017.

Analysis of the 2014 field collected data identifies three distinct riparian vegetation communities that occur 

along the river below Glen Canyon Dam. These different communities may respond to dam operations 

differently. A manuscript identifying, describing, and discussing the importance of these groups to monitoring 

and research is currently being developed.

A Techniques and Methods document describing the riparian vegetation monitoring methods was submitted 

for external review. A methods comparison was subsequently conducted in GCNRA in June to address 

reviewer comments. Initial analyses indicate that these methods are appropriately reliable, but a full analysis 

will be included in the Techniques and Methods document as an appendix. This will also be accompanied by 

the result of power analyses, which are being conducted to confirm necessary sample sizes.

Work identifying and refining vegetation-flow response guilds is being continued by collaborators. 

Collaborators at NAU, funded by USGS through the WaterSMART Program, completed a thesis and are 

working on two manuscripts for publication that investigate the functional traits of over 100 species that occur 

along the Colorado River through Grand Canyon. These data allow species to be placed in functional guilds 

more accurately, which improves the strength of models predicting the frequency of functional guilds in 

Figure 2. Vegetation cover is generally lower between the LCR and 

National Canyon. Shown is a debris fan at river mile 112.8R on 

8/31/2016

Figure 3. Woody vegetation is greater on sandbars in Marble Canyon 

than downstream of the LCR. Shown in Nautiloid (river mile 35.iL) on 

10/3/2016.
84

relation to dam operations. Using these newly acquired data, USGS and Forest Service collaborators are 

reanalyzing the vegetation-flow response guilds and developing models of probable frequencies of those 

guilds given different flow regimes.

In the next year, we will be moving forward with publishing the Techniques and Methods monitoring 

protocol, publishing the manuscript describing and evaluating the riparian floristic communities, and 

completing the manuscripts identifying and modeling the vegetation-flow response guilds. Annual monitoring 

will take place in Aug – Oct of 2017 in both Glen and Grand Canyons. Continued annual monitoring of 

riparian vegetation should allow us to examine the influence of flow regime on riparian vegetation cover and 

composition.

Project Element 11.2. Periodic landscape scale vegetation mapping and analysis using Remotely Sensed 

Data

The overall goal of this project element is to map changes in woody vegetation at the landscape scale through 

image processing, classification, and analysis. The specific objectives of the element are:

1. To produce an accurate classification of vegetation from the imagery acquired with the remote 

sensing overflight in 2013. 

2. To quantify stability and changes in vegetation composition from the classifications of vegetation 

completed for imagery acquired in 2002 to 2013. 

3. To cross-walk the composition of vegetation in the image-based classes from 2013 and 2002 with 

composition of response guilds identified in Element 11.1.

4. To detect and map tamarisk leaf beetle effects for remotely sensed vegetation canopies from 

overflight imagery from 2009 to 2013.

We are on track to accomplish these objectives by the end of the TWP (i.e., during FY17). The 

methodological steps required to accomplish objectives 1 and 2 were to first complete and publish the mosaic 

of overflight imagery acquired in 2013 (Durning et al. in press). Next was to complete and publish the total 

vegetation and river channel classification dataset from the 2013 image mosaic. These datasets are currently 

in review and nearing official USGS publication. The final step is to complete a classification of important 

riparian vegetation associations (groups of spectrally similar vegetation species) based on the 2013 image 

mosaic. This step is currently underway. We have quantified short-term (i.e., 2002 to 2013) and longer-term 

(1965-2013) stability and changes in total vegetation and presented these results at the Annual Reporting 

Meeting and the AMWG meeting in 2016. We have shown with this work that riparian vegetation has 

increased in area since completion of Glen Canyon Dam, and analysis of data acquired during the most recent 

overflight in 2013 shows that vegetation has continued to increase at elevations as low as below 24,000 CFS. 

Elevated base flows promote the expansion of riparian vegetation onto bare sand habitat and short pulses of 

high flow, such as controlled floods, do not keep vegetation from expanding onto bare sand habitat. We plan 

to quantify stability and changes in vegetation associations between 2002 and 2013 once the 2013 

classification is completed in the coming year. We then plan to complete the analyses for objective 3. 
85

Figure 4. Example of the 2013 imagery with automated total vegetation overlay (green). Image location is Colorado River and Little Colorado River 

confluence.

Finally, we have accomplished a great deal of work related to the fourth objective about detecting and 

mapping tamarisk leaf beetle effects from overflight imagery acquired in 2009 and 2013. We know for three 

important reaches of the river (areas surrounding Glen Canyon, Kanab Creek, and National Canyon) how 

much tamarisk exists based on detailed maps we’ve developed, and how much of this tamarisk was impacted 

by the beetle and defoliated during the growing season in 2013. We have shown with this work that the 

canopy cover of green, healthy tamarisk shrubs decreased from 2009 to 2013 and that this decreased the 

amount of leaf biomass on the shrubs and increased the amount of leaf biomass shed to the floodplain. We 

determined that on average, approximately 1/10th to 1/3rd of tamarisk in the study reaches were defoliated by 

the beetle at the time of the 2013 overflight. During FY17 we will expand the tamarisk defoliation mapping 

completed in the initial three reaches to the remainder of the river corridor. We also developed a method to 

make detailed maps of the amount of biomass associated with individual tamarisk trees in the Glen Canyon 

reach where we used lidar remote sensing data to enable this work. In the future, we hope to develop and 

implement a remote sensing-based method to monitor and map mortality of beetle-impacted tamarisk.

Eight products (papers, reports, theses, or datasets) from this project element have either already been 

published or are imminently pending (See table). 

Project Element 11.3 Influence of sediment and vegetation feedbacks on the evolution of sandbars in 

Grand Canyon since 1991 

Recent research in other large, eddy-dominated river systems has shown that vegetation influences the 

deposition of sediment and sediment deposition alters the location and types of riparian vegetation. Feedback 

loops between vegetation and sediment in Grand Canyon could be influencing the efficacy of high flow 

experiments and vegetation encroachment on camping areas.

The overall goal of this element is to understand the interplay between hydrology, vegetation and sediment 

dynamics among 20 sandbars for a 23-year period (1991 to 2013). The specific objectives of the element are:
86

1. How does establishment of vegetation nearer the channel (below stage at power plant capacity 

(31,000 ft3/s) influence sediment deposition on sandbars (net deposition and scour) associated with 

experimental high flows?

2. Does expansion of woody riparian vegetation below stage elevations of power plant capacity 

(31,000 ft3/s) and associated sediment response decrease shoreline complexity and negatively affect 

native fish rearing habitat (backwaters) and riparian habitat (compositional and structural 

complexity)?

3. In a regulated, debris fan-eddy river system, does expanded floodplain development on 

reattachment bars result in smaller eddy circulation zones and with reduced temporary storage 

capacity, or do river currents fundamentally change and affect sediment storage and transport 

capacity?

Data to support this project is being compiled. Historic vegetation data collected by Kearsley et al in the late 

1990’s and early 2000’s is being gathered, entered, and assessed for usefulness for this project. Additionally, 

survey data coincident with the intermittent vegetation data are being located and converted to a useable 

format.

This work was to be conducted by the Research Ecologist position, which has been vacant since August 2015. 

As such, this project has not started other than compiling historic data. Related work is being conducted as 

part of Project 3.3, and this project will incorporate those findings.

FY17 work will begin when a Research Ecologist starts and will have to begin with the FY15 and 16 tasks of 

parameter identification, determining the best methodology, and preliminary analysis of 4 sandbars. Hiring 

for the Research Ecologist position is on-going.

Project Element 11.4 Linking dam operations to changes in riparian biodiversity – the potential 

significance of vegetation change and insect emergence

The overall goal of this subproject is to quantify the strength of aquatic-terrestrial linkages and assess the 

relative importance of vegetation change and aquatic production in driving the population dynamics of a 

subset of the terrestrial fauna. The specific objectives of the element are:

1. Build a strong conceptual basis for understanding and analyzing linkages between flow 

management and riparian biodiversity in the Colorado River ecosystem

2. Determine the degree to which populations of terrestrial animals respond to spatial and temporal 

variation in aquatic insect emergence along the Colorado River, with an initial focus on the Glen and 

upper Marble Canyons.

3. Identify whether long-term changes in vegetation have influenced populations of terrestrial 

consumers, particularly birds and terrestrial insects in Glen Canyon.

4. To the extent possible, determine the links between terrestrial fauna and vegetation-flow response 

guilds.

In FY15, this project had minimal funding. With assistance from John Sabo, an aquatic-terrestrial expert at 

Arizona State University, we identified a graduate student, Christina Lupoli, who began work associated with 

this element in FY16 when there was sufficient funding. We were able to leverage funding available by ASU

such that Lupoli’s funding was half GCDAMP and the rest ASU. In FY16, Lupoli explored different research 

approaches at a low cost by joining already planned trips to Glen Canyon and downriver. In particular, she 

joined multiple trips to Glen Canyon Dam by the aquatic food base trip and joined downriver trips by Grand 
87

Canyon Youth, the Riparian Vegetation project and the Aquatic Foodbase project. The focus of research has 

been on documenting patterns in relative abundance of various terrestrial consumers as well as taking nonlethal tissue samples (i.e., fur from rodents and tail clippings from lizards) to determine the relative 

importance of terrestrial versus aquatic insects in the diet of these consumers. We are working to develop 

reliable relative population indices so we can compare patterns of small mammal, birds, bat, and lizard 

occurrence to patterns of aquatic insect production – both through space and time. 

Beginning in April 2016, we also deployed pitfall trap arrays at ten to fifteen sites throughout the Colorado 

River reach between Glen Canyon Dam and Badger Rapid, concurrent with monthly sticky trap monitoring. 

The goal of pitfall trapping is to collect terrestrial arthropods, which will be used to quantify the relative 

magnitude of aquatic resource usage in terrestrial arthropod food webs. Sample collection, processing, 

identification, and preparation for stable isotope analysis is ongoing. In addition, on downriver trips, tissue 

samples were taken from 128 lizards across five species (Uta stansburiana - Common Side-blotched lizard; 

Sceloporus magister - Desert spiny lizard; Urosaurus ornatus - Ornate tree lizard; Phrynosoma platyrhinos 

calidiarum - Southern desert horned lizard; Aspidoscelis tigris - Tiger Whiptail) and 75 rodents across four 

species (Reithrodontomys megalotis - Western harvest mouse; Peromyscus crinitus - Cactus mouse; 

Peromyscus eremicus - Canyon mouse; Dipodomys merriami - Merriam’s Kangaroo Rat) and are currently 

being analyzed alongside samples of vegetation, terrestrial insects, including spiders, and aquatic insects.

Project Element 11.5. Science Review Panel of Successes and Challenges in Non-native Vegetation 

Control in the Colorado River and Rio Grande Watersheds

This workshop took place in June 2015. A publication of the extended abstracts from the riparian restoration 

workshop is underway. It is anticipated to be available as a USGS Open-File Report in spring 2017. Work on 

this aspect of the work plan, and several others, has been delayed due to the Research Ecologist position being

vacant since August 2015. A second workshop that was proposed has not taken place due to the lack of 

personnel and funding.
88

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations Comments

Dataset

Palmquist, E.C., Ralston, 

B.E., Sarr, D., Merritt, 

D., Shafroth, P.B., and 

Scott, 

J.A., 2016, Southwestern rip

arian plant trait matrix, 

Colorado River, Grand 

Canyon, 2014 to 2016-Data: 

U.S. Geological Survey data 

release, http://dx.doi.org/10.

5066/F7QV3JN1.

Aug 2016

Journal

Palmquist, E.C., Ralston, 

B.E., Sarr, D., Merritt, 

D., Shafroth, P.B., and 

Scott, J.A., Functional traits 

and ecological affinities of 

riparian plants along the 

Colorado River in Grand 

Canyon

Early 2017 In press, Western North 

American Naturalist.

Techni

ques 

and 

Metho

ds

Palmquist, E.C., Ralston, 

B.E., Sarr, D., and Johnson, 

T.C., in revision, 

Monitoring Riparian 

Vegetation Composition 

and Cover along the 

Colorado River downstream 

of Glen Canyon Dam

Oct 2017 Submitted for review Jan 

2016, in revision.

Journal

Sarr, D.A., D.M. Merritt, E. 

C. Palmquist, J.A. Scott, 

P.B. Shafroth, B.E. Ralston, 

TE. Kolb, and M. McCoySulentic, in prep, Riparian 

flow-response guilds for a 

large regulated river in the 

arid southwest

May 2017

Unexpected loss of lead 

author, currently being 

completed by collaborators.

Journal

D.M. Merritt, J.A. Scott, E. 

C. Palmquist, P.B. Shafroth 

and B.E. Ralston, In prep, 

Riparian flow-response 

guilds: a management tool 

To be 

submitted 

summer 

2017

Lead author D. Merritt 

(USFS), outgrowth of the 

guild identification project.
89

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations Comments

to predict vegetation change 

along a regulated river.

Journal

McCoy-Sulentic, M., Kolb, 

T., Merritt, D., Palmquist, 

E., Ralston, B, and Sarr, D., 

in review, Habitat variation 

in species-level plant 

functional traits along the 

Colorado River, Grand 

Canyon

Sept. 2017

Submitted to Ecology and 

Evolution. Project funded by 

WaterSMART, but 

contributing to GCMRC 

riparian vegetation 

monitoring.

Journal

McCoy-Sulentic, M., Kolb, 

T., Merritt, D., Palmquist, 

E., Ralston, B, Sarr, D., and 

Shafroth, P., in review, 

Changes in communitylevel riparian plant traits 

over hydrologic zones and 

inundation gradients, 

Colorado River, Grand 

Canyon

Sept. 2017

Submitted to Wetlands. 

Project funded by 

WaterSMART, but 

contributing to GCMRC 

riparian vegetation 

monitoring.

Journal

Palmquist, E.C., Ralston, 

B.E., Merritt, D., and 

Shafroth, P.B., Landscape 

scale processes influence 

riparian plant composition 

along a regulated river: 

Implications for research 

and management.

Oct 2017 In prep, to be submitted to 

Journal of Arid Environments.

Data 

Series 

Report

Durning, L.E., Sankey, J.B., 

Davis, P.A., Sankey, T.T., 

2016 (in press). Four-band 

image mosaic of the 

Colorado River corridor 

downstream of Glen 

Canyon Dam in Arizona, 

derived from the May 2013 

airborne image acquisition: 

U.S. Geological Survey 

Data Series ####, xx p., 

Dec. 2016 Currently in press
90

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations Comments

http://dx.doi.org/10.3133/ds

####.

Dataset

Durning, L.E., Sankey J.B., 

Davis, P.A., Sankey, T.T., 

2016, Four Band Image 

Mosaic of the Colorado 

River Corridor in Arizona, 

2013, including Accuracy 

Assessment Data: U.S. 

Geological Survey data 

release, 

http://dx.doi.org/10.5066/F7

TX3CHS

Dec. 2016 Currently in press

M.S. 

Thesis

Bedford, A. "Remote 

Sensing of Tamarisk 

(Tamarix spp.) defoliation 

by the Tamarisk Leaf Beetle 

(Diorhabda carinulata) 

along the Colorado River in 

Arizona " M.S. Thesis. 

Northern Arizona 

University, May 2016

May 2016 Advised by E. Scheifer, T 

Sankey, J Sankey, B Ralston

Journal 

Article

Sankey, TT, Sankey, JB, 

Bedford, A, Horne, R, 2016, 

Remote sensing of tamarisk 

biomass, insect herbivory, 

and defoliation: novel 

methods and applications in 

the Grand Canyon region, 

Arizona, USA. 

Photogrammetric 

Engineering and Remote 

Sensing 82(8), pp. 645-652, 

doi: 

10.14358/PERS.82.8.645

Aug 2016

Journal 

Article

Sankey, J. B., B. E. Ralston, 

P. E. Grams, J. C. Schmidt, 

and L. E. Cagney (2015), 

Riparian vegetation, 

Colorado River, and 

climate: Five decades of 

June 2015
91

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations Comments

spatiotemporal dynamics in 

the Grand Canyon with 

river regulation, Journal of 

Geophysical Reseach 

Biogeosciences, 120, 1532–

1547, 

doi:10.1002/2015JG002991.

Dataset

Sankey, J.B., Ralston, B.E., 

Grams, P.E., Schmidt, J.C., 

and Cagney, L.E. 2015. 

Riparian vegetation, 

Colorado River, and 

climate: Five decades of 

spatiotemporal dynamics in 

the Grand Canyon with 

river regulation - Data: U.S. 

Geological Survey data 

release, 

http://dx.doi.org/10.5066/F7

J67F0P.

June 2015

Dataset

Durning, et al, in review, 

2013 image mosaic total 

vegetation classification 

dataset

Jan. 2017 Currently in review

Dataset

Durning, et al, in review, 

2013 image mosaic water 

classification dataset

Jan. 2017 Currently in review

Openfile 

Report

Ralston, B. and Sarr, 

D. Case Studies of 

Riparian and Watershed 

Restoration in the 

Southwestern United 

States: Principles, 

Challenges, and Successes.

April 2017 Delayed due to loss of D. Sarr
92

Project 11 Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $244,300 $13,500 $7,500 $139,500 $6,800 $35,976 $447,576 

Actual

Spent $181,180 $4,711 $5,734 $168,279 $0 $28,011 $387,914 

(Over)/Under

Budget $63,120 $8,789 $1,766 ($28,779) $6,800 $7,965 $59,662 

FY15 

Carryover $48,929 CPI Decrease ($22,660) FY16 Carryover $85,931 

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Salary costs reduced due to vacancy.

- Cooperative agreement expenses increased due to additional funding for MS student.

- Costs to other USGS cost centers decreased due to other center direct charging our project.

- Carryover will be used to fill vacancy and catch up on delayed work due to vacancy.
93

FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 12: Changes in the Distribution and Abundance of Culturally-Important Plants in the Colorado 

River Ecosystem: A Pilot Study to Explore Relationships between Vegetation Change and Traditional 

Cultural Values

Program Manager 

(PM) Helen Fairley Investigator(s) (I) Helen Fairley, USGS, GCMRCPeter Bungart, Hualapai Tribe

Tony Joe, Navajo Nation

Michael Yeatts, Hopi Tribe

Daniel Sarr, USGS, GCMRC

Charles Yackulic, USGS, 

GCMRC

Email hfairley@usgs.gov

Telephone (928) 556-7285

SUMMARY

Introduction

Project 12 aims to answer a single, broad research question: How have culturally-valued vegetation attributes 

of the riparian landscape of the Colorado River corridor changed since closure of Glen Canyon Dam, and how 

have those changes affected cultural resource values that are important to Native American tribes? The 

intention of this research effort is two-fold: 1) document where and how dam operations have affected 

culturally-important riparian plants in the Colorado River corridor, and 2) lay a foundation of knowledge to 

support future restoration work that may be undertaken by the tribes and/or National Park Service to help 

maintain important qualities of the riparian ecosystem.

As originally conceived, this project involved two elements, each requiring a different approach: 1) an 

assessment of changes in vegetation in the Colorado River corridor below Glen Canyon Dam that relate to 

some of the expressed cultural interests of the Native American tribes involved in the Glen Canyon Dam 

Adaptive Management Program (GCDAMP), thereby creating a bridge between scientific and traditional 

knowledge systems; and 2) an assessment of how these changes may have affected (either positively or 

negatively) culturally-important aspects of the landscape valued by these same groups. 

The first phase encompassed three primary objectives: 

1) engage tribes in a collaborative research effort to identify changes in the riparian ecosystem of the 

Colorado River corridor that may have affected cultural values and resources that contribute to the 

identification of Grand Canyon as a Traditional Cultural Property; 

2) compile and synthesize data about riparian vegetation and specific species of cultural importance to 

tribes from a variety of existing sources, including but not limited to, previous Glen Canyon 

Environmental Studies (GCES)-era studies, existing GCMRC and tribal monitoring data, published 

articles, historical journals and oblique historical imagery; and 

3) analyze these data to evaluate the previous distribution and comparative abundance of targeted 

(culturally-important) plant species throughout the river corridor landscape in comparison with 

current conditions.
94

The second phase of this project proposed to use the information obtained in Phase 1 to develop culturallyappropriate methods for eliciting tribal perspectives about the changes that have occurred to culturallyimportant important plant species and then use those methods to evaluate how the changes may have affected 

cultural landscape values important to each of the tribes. Specific methods to be employed in Phase 2 were to 

be determined collaboratively with tribal participants after they have had a chance to review the results of 

Phase 1 and had engaged in further discussion about possible future methodological approaches. Since 

initiation of the project in FY15, there has been a significant turn-over in tribal personnel, and several tribes 

that were formally supportive of this project have recently indicated that they no longer wish to participate in 

it. In addition the lack of a riparian ecologist at GCMRC throughout FY16, further hampered our ability to 

complete the project in FY16 as originally envisioned. This project now focuses primarily on completing 

Phase 1 research objectives and is anticipated to be completed in FY17.

Phase 1 Accomplishments

In February 2015, GCMRC hosted the first of two planned workshops. During this workshop, plant species of 

mutual interest to multiple tribes were discussed, and a list of plants was identified to be the focus of the pilot 

study (Table 1).

Table 1. Targeted riparian species of the Project 12 pilot study 

Goodding’s willow (Salix gooddingii)

Cottonwood (Populus fremontii)

Netleaf Hackberry (Celtis reticulata)

Honey Mesquite (Prosopis glandulosa)

Coyote willow (Salix exigua)

Seep-willow (Baccharis emoryi, B.salicifolia)

Apache plume (Fallugia paradoxa)

Prince’s plume (Stanleya pinnata)

Arrow-weed (Pluchea sericea)

Common reed (Phragmites australis)

Cattail (Typha sp.)

Horsetail (Equisetum sp.)

Dropseed (Sporobolus sp.)

Indian Rice Grass (Achnatherum hymenoids) 

In FY16, Fairley continued worked started in FY15 by compiling available data on this list of targeted 

species, drawing upon a variety of existing information sources. Data sources included prior GCES-era and 

GCDAMP-sponsored research articles and reports, GCMRC and tribal monitoring program data, and 

historical river runner journals. In addition, starting in late summer 2015 and continuing in FY16, Fairley

located historical imagery that could be analyzed for changes in vegetation through time. In addition to 

working with an existing collection of matched images from the Desert Laboratory Repeat Photography 

collection, in November 2015, high-resolution digital scans of several hundred photographs from the 1923 

USGS Birdseye expedition were obtained.

After identifying the whereabouts of historical photographs and assessing their condition and suitability for 

documenting vegetation changes, Fairley began applying analytical methods previously developed by Webb 

(1996) to evaluate vegetation changes by comparing the 1890 Stanton photos with 1990–1992 replicates and 

also comparing the 1990–1992 matches with duplicate images obtained in 2010–2011. This analysis work 

began in late summer of 2015, continued intermittently in FY2016, and is ongoing. The analysis identifies 

whether the plants of cultural value to the tribes are present in the photographs, are located in the same areas 
95

as in the past, and whether their abundance has increased or decreased in each photograph according to a 

simple ranked scale (e.g., no apparent increase/decrease, small increase or decrease (<25% change in numbers 

of individuals or total cover) or large increase or decrease (>25% change). It also evaluates changes in the 

physical context of where specific plants grow, noting any apparent physical changes to local context 

associated with observed plant changes (e.g., differences in presence or absence of sand deposits, evidence of 

debris flows or rock falls, changes in biological soil crust cover, etc.)

In addition to the photographic analysis, Fairley began compiling a bibliography of journal articles and other 

reference materials about each of the targeted species in FY16. Because the aim of this bibliography is to 

serve as a resource for future restoration efforts along the Colorado River, it primarily focuses on articles that 

document life history characteristics of each species and their adaptions to specific environmental conditions 

that encourage or discourage their propagation and long-term survival. For example, studies by Shafroth and 

others (1998, 2010) discuss how the rate of flood recession affects propagation of Goodding’s willow, 

tamarisk, and cottonwood, and how burial by flood sediments appears to favor the survival of young shoots of 

native species such as Goodding’s willow over tamarisk. For some species, such as cottonwood and 

phragmites, the available literature is extensive, and in these cases, only a subset of available journal articles 

is included in the bibliography, while for other species, such arrow-weed, very little published information is 

currently available. The gaps in available knowledge about specific species highlight areas that could 

potentially be filled by focused studies conducted through the GCDAMP. 

In May 2016, in conjunction with the Project 4 river trip, Fairley worked with a volunteer photographer to 

begin matching photographs from the 1923 expedition. Approximately 40 photographs have been matched to 

date. All of them show increases in woody riparian vegetation within the former flood scour zone of the predam Colorado River. Examples of two of these recently obtained matches is provided below (figures 1 and 2).

Figure 1. Matched view at river mile 126.1, right bank. Top photograph by E.C. LaRue, September 6, 1923. Bottom photograph taken by A. H. Fairley 

on May 10, 2016. Note that the 2016 view of the river is now obscured by dense, woody riparian vegetation dominated by tamarisk, arrow-weed, and 

seep-willow.
96

Figure 2. Matched view at river mile 197.0, left bank. Top photograph by E. C. LaRue, September 25, 1923. Bottom photograph taken by A.H. Fairley 

on May 11, 2016. Note in the 2016 view that the Goodding’s willow tree is no longer present and a dense thicket of arrow-weed, and seep-willow now 

occupies the formerly shaded, open sandy shoreline. 

Preliminary Conclusions

As of September 2016, approximately 35% of the Stanton collection had been systematically analyzed. The 

analysis completed to date shows that riparian vegetation has increased dramatically since 1889/1890 and that 

it has continued to increase since implementation of the GCDAMP in the mid-1990s. Woody native riparian 

shrubs -- specifically seep-willow.—increased significantly between the early 1990s and 2010–2011, while 

coyote-willow and non-native tamarisk increased at a slower rate. Netleaf hackberry increased between 

1889/90 and the early 1990s, with diminished increases thereafter, while Goodding’s willow has decreased 

substantially since 1889/90.

While this analysis was underway, Fairley learned that a similar study with a somewhat different (broader 

biology-focused) emphasis and methodology had been initiated by Dr. Michael Scott and colleagues, using a 

sample of the Stanton photographs and rematches from the early 1990s and 2010-2011. Fairley subsequently 

collaborated with Dr. Scott and other coauthors in preparing a book chapter based on the results of this study 

(Scott et al., in review). Some of the conclusions from analysis of the sample of repeat photographs include 

the following:

1) Woody riparian vegetation has increased throughout the river corridor in Grand Canyon between 

the 1990s and 2012. In general, total woody riparian vegetation, including tamarisk, showed increased 

cover and density during this period in 89.3% of the matched images from 2010-12, with seep-willow 

increasing in 53.4% of the views over the past 20 years. Previous speculation that coyote willow 

might gradually replace tamarisk under the post-dam flow regime (Stevens 1989) is not born out by 

the photographic evidence, as only ~2% of the 2010-2012 photos show noticeable increases in coyote 

willow. It should be noted, however, that this species can be difficult to detect in photographs with 

dense riparian vegetation. 
97

2) Gains in riparian vegetation cover over the past two decades were primarily below the maximum 

stage of post-dam controlled floods (1,274 m3/s), especially in near-shore locations for species like 

tamarisk, seep-willow, and arrow-weed. 

3) Some of the increase in riparian vegetation in the new high-water zone below the stage of the 1983 

flood (2,747 m3

/s) is due to the encroachment of species that are more commonly found in the old 

high-water zone, such as honey mesquite and desert broom.

4) In contrast to observed vegetation increases, 9.4% of the rematches in 2010-12 show no apparent 

change, and < 2% of the views show a decrease in woody riparian vegetation cover and density. 

Photographs that show little or no change are primarily located in narrow, canyon-bound sections of 

the river corridor, suggesting these settings may not be conducive to the establishment of persistent 

riparian vegetation.

5) Disconnection of the old high-water assemblage from modern river flows has left certain species 

like honey mesquite vulnerable to drought stress. The historic photographic evidence, coupled with 

other lines of evidence (e.g., Sankey et al. 2015), show a decline in vegetated cover in the old high 

water zone since the early 1990s. The work of Webb (1996) indicates that certain high water zone 

species such as catclaw acacia (Acacia greggii) may be less affected by drought than other long-lived 

species, such as mesquite.

6) In addition to the natural establishment of riparian vegetation in the new high water zone, some 

non-native species like tamarisk and Russian-olive (Elaeagnus angustifolia) have been deliberately 

removed from some places in the river corridor while native vegetation has been planted in other 

locations as experiments or pilot restoration efforts in Marble and Grand Canyons. The artificial 

manipulation of river corridor vegetation needs to be systematically tracked and mapped, and specific

activities and locations of vegetation manipulation should be clearly documented in readily accessible 

reports, so that cause-and-effect relationships between flow management and vegetation response can 

be accurately assessed in the future. 

7) Whether HFEs have been a factor in the recent expansion of riparian vegetation is currently 

unknown and will require careful, real-time monitoring of vegetation following HFEs or retrospective 

analyses examining the age structure of encroaching vegetation. The seasonal timing of HFEs also 

warrants further study as timing of high flows could preferentially shift the structure and composition 

of riparian vegetation.

Next steps

In FY17, using carry-over funds from FY16, we will complete the species-specific analysis using repeat 

photographs, and will continue to match and analyze additional photographs from the 1923 expedition. In 

2017, in collaboration with Dr. Scott, we will report the results of this analysis in a peer-reviewed journal 

article. This article will expand upon the initial conclusions reached from analyzing a sample of the Stanton 

photographs and will focus in more detail on the changes in abundance and distribution of each of the species 

identified in the FY15 workshop, so as to provide a more comprehensive assessment of the changes in the 

distribution and abundance of culturally-valued riparian species along the Colorado River corridor.

References 

Sankey, J.B.; Ralston, B.E.; Grams, P.E.; Schmidt, J.C.; Cagney, L.E. 2015. Riparian vegetation, Colorado 

River, and climate: Five decades of spatiotemporal dynamics in the Grand Canyon with river 

regulation. Journal of Geophysical Research: Biogeosciences. 120: 1532–1547.
98

Scott M.L., Webb R.H., Johnson R.R., Turner R.M., Friedman J.M., and Fairley H.C. In review. Evaluating 

Riparian Vegetation Change in Canyon-bound Reaches of the Colorado River Using Spatially 

Extensive Matched Photo Sets. Chapter 18. In: Johnson R.R., Carothers S.W., Finch, D.M., and 

Kingsley, K.J., 20XX. Riparian Ecology: Past, Present, Future. Gen. Tech. Rep. RMRS-GTRXXXX. Fort Collins, CO: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research 

Station.

Shafroth, P.B., Auble, G.T., Stromberg, J.C., and Patten, D.T., 1998, Establishment of woody riparian 

vegetation in relation to annual patterns of streamflow, Bill Williams River, Arizona. Wetlands 18: 

577-590.

Shafroth, P.B.; Wilcox, A.C.; Lytle, D.A.; Hickey, J.T.; Anderson, D.C.; Beauchamp, V.B.; Hautzinger, A.; 

McMullen, L.A.; Warner, A. 2010. Ecosystem effects of environmental flows: modelling and 

experimental flood in a dryland river. Fresh Water Biology. 55: 68-85.

Stevens, L.E. 1989. Mechanisms of riparian plant community organization and succession in the Grand 

Canyon, Arizona. Dissertation. Flagstaff, AZ. Northern Arizona University. 115 p.

Webb, R.H., 1996, Grand Canyon: A Century of Change, Rephotography of the 1889-1890 Stanton 

Expedition. University of Arizona Press, Tucson, 290 p.
99

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Presentation

Dam-induced changes to 

riparian ecosystems and 

associated traditional 

cultural values downstream 

of Glen Canyon Dam, 

Arizona: a progress report 

on a pilot study integrating 

science and traditional 

ecological knowledge. 

10/8/15

Fairley, H.C., 2015, 

Dam-induced changes to 

riparian ecosystems and 

associated traditional 

cultural values 

downstream of Glen 

Canyon Dam, Arizona: a 

progress report on a pilot 

study integrating science 

and traditional ecological 

knowledge. Oral 

presentation at the 13th 

Biennial Conference of 

Science and Management 

on the Colorado Plateau, 

Flagstaff, Arizona, 

October 6, 2015.

Chapter in 

edited 

volume

Evaluating Riparian 

Vegetation Change in 

Canyon-bound Reaches of 

the Colorado River Using 

Spatially Extensive Matched 

Photo Sets

9/15/16

Scott M.L., Webb R.L., 

Johnson R.R., Turner 

R.M., Friedman J.M., 

and Fairley H.C. In 

review. Evaluating

Riparian Vegetation 

Change in Canyon-bound 

Reaches of the Colorado 

River Using Spatially 

Extensive Matched Photo 

Sets. Chapter 18. In: 

Johnson R.R., Carothers 

S.W., Finch, D.M., and 

Kingsley, K.J., 20XX. 

Riparian Ecology: Past, 

Present, Future. Gen. 

Tech. Rep. RMRS-GTRXXXX. Fort Collins, 

CO: U.S. Department of 

Agriculture, Forest 

Service, Rocky Mountain 

Research Station.
100

Project 12 Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $20,000 $2,500 $5,500 $45,000 $0 $4,705 $77,705 

Actual

Spent $19,542 $2,278 $12,529 $0 $0 $4,116 $38,464 

(Over)/Under

Budget $458 $222 ($7,029) $45,000 $0 $589 $39,241 

FY15 

Carryover $21,917 CPI Decrease ($3,934) FY16 Carryover $57,224 

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Operating expenses increased due to a contract to organize and upgrade the database associated with the 

Desert Laboratory repeat photo collection.

- Cooperative agreements decreased due to a decision by tribal participants to not be cooperators in Phase II 

of this project. Unspent funds will be used to support additional work on the photo collection, travel, salary 

and river logistics associated with completing the photo matching component of this project in 2017.
101

FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 13: Socioeconomic Monitoring and Research

Program Manager 

(PM) Lucas Bair Investigator(s) (I) Lucas Bair, USGS, GCMRCCharles Yackulic, USGS, 

GCMRC

John Duffield, Univ. Of Montana

Chris Neher, Univ. Of Montana

David Patterson, Univ. Of 

Montana

Michael Springborn, UC Davis

Craig Bond, Pardee RAND

Mathew Reimer, UA Anchorage

Email lbair@usgs.gov

Telephone (928) 556-7362

SUMMARY 

Summary of FY15–17 Goals and Objectives

The overall objective of Project 13 is to identify recreational and tribal preferences for, and values of, 

downstream resources and evaluate how preferences and values are influenced by Glen Canyon Dam (GCD) 

operations. In addition, Project 13 is integrating economic information with data from long-term and ongoing 

physical and biological monitoring and research studies led by the Grand Canyon Monitoring and Research 

Center (GCMRC) to develop tools for scenario analysis to improve the ability of the Glen Canyon Dam 

Adaptive Management Program (GCDAMP) to evaluate and prioritize management actions, monitoring and 

research.

Project 13 involves three related socioeconomic monitoring and research studies. These studies include: 

(13.1) evaluation of the impact of GCD operations on regional economic expenditures and economic values 

associated with angling in Glen Canyon National Recreation Area (GCNRA) downstream from GCD, and 

whitewater floating in Grand Canyon National Park (GCNP) that begins at Lees Ferry; (13.2) assessment of 

tribal preferences for, and values of, downstream resources as impacted by GCD operations; and (13.3) 

development of scenario analysis methods and tools, using economic metrics, to inform management actions 

and prioritize monitoring and research on resources downstream of GCD.

Summary of Activities Completed and Relevant Accomplishments

Project Element 13.1

Angler interviews were initiated at Lees Ferry in Glen Canyon National Recreation Area during the spring of 

2015 in cooperation with the Arizona Game and Fish Department. Anglers were intercepted on the river to 

obtain creel, name, and mailing address information. Interviews continued into early Fall 2016. 

Grand Canyon National Park private whitewater floater name and address information was collected from the 

National Park Service in October, 2015. The sample included 1,425 individuals who participated in 

whitewater trips in Grand Canyon between September 2014 and August 2015. 
102

Office of Management and Budget clearance was 

received for the study. In-depth surveys were 

mailed to anglers and whitewater floaters early in 

FY16. Data entry and analysis occurred in the 

spring of FY16. The final report detailing the 

study results was submitted to the Bureau of 

Reclamation. 

Highlights from the data collection include: 

• Collaboration with Arizona Game and Fish 

Department was established and sharing of 

methods, practices, and creel survey data 

continues.

Project Element 13.2

Project 13.2 is scheduled to be implemented in FY17. Meetings to discuss details of Project 13.2 with 

Tribal representatives to the GCDAMP and Tribal staff occurred in FY16:

• Lucas Bair from GCMRC participated in Project 13.2 discussions at the Hopi Cultural Preservation 

office on February 8, 2016, at a Zuni Cultural Resources Advisory Team meeting on March 3, 2016 

and with Navajo Adaptive Management and Technical Work Group representatives on April 20, 

2016. 

Project Element 13.3

A bioeconomic model was developed to identify the economically preferred management strategy for 

established nonnative fish to achieve humpback chub survival targets. The model was completed and the 

manuscript stemming from this work will be submitted in December 2016. In FY17 the model will be 

expanded to include the following: 1) evaluating parameter uncertainty to aid in the identification and 

prioritization of monitoring and research of native and non-native fish; and 2) assisting in the experimental 

design of future management experiments in the Glen Canyon Dam Long-Term Experimental and 

Management Plan Environmental Impact Statement (LTEMP EIS) (e.g. trout management flows). 

Summary of Reports and Products

Project Element 13.1

The results of the angler and whitewater floater surveys identified regional expenditures in local counties 

(Coconino, Mohave and Navajo Counties, AZ, Kane, San Juan and Washington Counties, UT; and Clark 

County, NV) and net economic value (NEV) per trip of each recreational activity over a range of average 

Colorado River flows (cfs) (Duffield et al. 2016).

Regional Expenditures

• Guided anglers on average spent $1,101 per trip with $861 of these expenditures spent locally. 

• Non-guided anglers on average spent $369 per trip with $268 of these expenditures spent locally.

• Private whitewater floaters on average spent $1,634 per trip with $969 of these expenditures spent 

locally.

Net Economic Value
103

NEV is the amount of money recreationists would be willing to spend in additional to what they already spent 

on their trip. 

• For anglers, NEV ranges from $87 - $432 per trip, depending on average Colorado River flow (cfs). 

Ranking of flow scenario NEV is consistent with Bishop et al. 1987 (Figure 1).

Figure 1 Angler net economic values across a range of average Colorado River flows. The data was generated from two surveys conducted in Glen 

Canyon National Recreation Area.

• For whitewater floaters, NEV ranges from $603 - $1,237 per trip, depending on average Colorado 

River flow measured in cubic feet per second (cfs). The whitewater floaters highest NEV is at 22,000 

cfs. Ranking and magnitude of flow scenario NEV is consistent with Bishop et al. 1987 (Figure 2).

Figure 2 Private whitewater floater net economic values across a range of average Colorado River flows. The data was generated from two surveys 

conducted in Grand Canyon National Park.

Project Element 13.3

The modeling objective is to identify the least-cost management strategy that reduces downstream rainbow 

trout (trout) abundance to achieve mainstem annual juvenile humpback chub (chub) survival targets, which 

are set to meet chub population recovery goals. The model integrates an abridged version of the LTEMP EIS 

chub and trout population models, where trout populations in the Juvenile Chub Monitoring (JCM) reach 

trigger the number of removal trips in a year. The model captures uncertainty over annual trout recruitment in 

the tailwater of GCD. 
104

Preliminary results indicate that the least-cost management strategy to achieve juvenile chub survival goals 

requires trout removal over a limited range of trout abundance.2 For example, under this strategy, trout 

removals would not be conducted when the numbers of trout in the JCM reach are below 1,238 or above 

2,622. Instead, removals would be performed 4-6 times per year, with the number of removals increasing with 

increasing trout abundance in the JCM reach (Figure 3).

Figure 3 Least-cost trout removal strategy to achieve juvenile chub survival goals.

Next Steps

Project Element 13.1

• Next steps may include updating and expanding on the Glen Canyon and Grand Canyon Recreation 

Economic Utility that was developed for the LTEMP EIS (Interior 2016). This would provide a tool 

for the GCDAMP to conduct scenario analysis to assess the impacts of GCD operation on recreation 

in Glen and Grand Canyons, with up-to-date recreation economic data.

Project Element 13.2

• Project 13.2 is scheduled to be implemented in FY17.

Project Element 13.3

• Identify the importance of parameter uncertainty on the sensitivity of cost-effective outcomes in the 

bioeconomic model. Evaluating parameter uncertainty will aid in the identification and prioritization 

of monitoring and research of native and non-native fish.

• Incorporate additional non-native fish management actions and associated costs in the bioeconomic 

model, such as trout management flows at GCD, to identify the most cost-effective management 

alternatives to achieve juvenile chub survival targets under various future scenarios. This inform on 

future native and non-native fish management and other LTEMP EIS experiments.

 2 This information is preliminary. Final results will be present pending updated juvenile humpback chub field data 

collected during the summer of 2016.

500 1000 1500 2000 2500 3000

0 1 2 3 4 5 6

Observed Trout in Juvenile Chub Monitori 

Annual Removals
105

References

Bair, L.S., D.L. Rogowski, and C. Neher. 2016. Economic value of angling on the Colorado River at Lees 

Ferry: using secondary data to estimate the influence of seasonality. North American Journal of Fisheries 

Management 36(6) 

Bishop, R.C., K.J. Boyle, M.P. Welsh, R.M. Baumgartner, and P.C. Rathbun. 1987. Glen Canyon Dam 

releases and downstream recreation: an analysis of user preferences and economic values. Glen Canyon 

Environmental Studies Report, 27, 87.

Duffield, J., C. Neher, and D. Patterson. 2016. Economic analysis of Glen Canon angler and Grand 

Canyon whitewater visitor surveys. University of Montana.

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Presentation Bioeconomic Model of 

Rainbow Trout 

(Oncorhynchus mykiss) and 

Humpback Chub (Gila cypha) 

Management in the Grand 

Canyon. 

NA June 2016 NA Bair, L., C. Yackulic, M. 

Springborn, M. Reimer, 

and C. Bond. 

Presentation at 

Association for the 

Sciences of Limnology 

and Oceanography. Santa 

Fe, NM.

Presentation Bioeconomic Model of 

Rainbow Trout 

(Oncorhynchus mykiss) and 

Humpback Chub (Gila cypha) 

Management in the Grand 

Canyon. 

NA June 2016 NA Bair, L., C. Yackulic, M. 

Springborn, M. Reimer, 

and C. Bond. 

Presentation at World 

Conference on Natural 

Resource Modeling. 

Flagstaff, AZ. June 16, 

2016.

Report Economic Analysis of Glen 

Canyon Angler and Grand 

Canyon Whitewater Visitor 

Surveys

FY 

16

September 

2016

FY 16 Duffield, J., C. Neher, 

and D. Patterson. 

University of Montana.

Journal 

manuscript

Economic Value of Angling 

on the Colorado River at Lees 

Ferry: Using Secondary Data 

to Estimate the Influence of 

Seasonality

Extr

a 

prod

uct 

no 

date

Published 

September 

2016

FY 16 Bair, L., D. Rogowski, 

and C. Neher. This is a 

manuscript that is an 

outgrowth of Project 

13.1.
106

PRODUCTS/REPORTS

Type Title Due 

Date

Date 

Delivered

Date 

Expected Citations/Comments

Journal 

manuscript

Enhancing native species 

population viability via costeffective invasive species 

control in the Grand Canyon, 

USA

FY 

15-

17

Anticipate

d 

submissio

n 

December 

2016

FY 16-17 Bair, L., C. Yackulic, M. 

Springborn, M. Reimer, 

and C. Bond. In 

preparation.

Project 13 Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $124,900 $10,000 $800 $54,000 $0 $17,881 $207,581 

Actual

Spent $126,087 $5,235 $22,628 $36,000 $0 $19,528 $209,479 

(Over)/Under

Budget ($1,187) $4,765 ($21,828) $18,000 $0 ($1,647) ($1,898)

FY15 

Carryover $9,296 CPI Decrease ($10,510) FY16 Carryover ($3,111)

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Operating expenses increased and cooperative agreement expenses decreased due to contracting with one 

"Cooperator" rather than entering into a cooperative agreement.

- Shortfall will be made up with Project 15 carryover.
107

FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 14: Geographic Information Systems (GIS) Services and Support

Program Manager 

(PM) Tom Gushue Investigator(s) (I) Tom Gushue, USGS, GCMRCTim Andrews, USGS, GCMRC

Email tgushue@usgs.gov

Telephone (928) 556-7370

SUMMARY

Geographic Information Systems (GIS) continues to play a critical role in nearly all of GCMRC’s science 

efforts and is prevalent in many of the projects proposed in the FY15–17 Triennial Work Plan (TWP). It is 

used across disciplines and is a powerful tool for integrating geospatial data collected by many different 

projects. The TWP has provided GCMRC an opportunity to develop a GIS project better designed to 

successfully function within GCMRC and meet the current and future needs of scientists, managers, and the 

public alike. Most work performed within this project falls within one of three main tenets: Geospatial Data 

Analysis, Geospatial Data Management, and Access to Geospatial Data Holdings. . This annual report affords 

us a chance to clearly define the work performed in each of these elements, accomplishments made over the 

past year, and how this work relates to both individual science projects and the GCMRC’s overall mission.

14.1. Geospatial Data Analysis: Support to Science Projects

The GIS Project continued to support other science projects through geospatial data processing and analysis 

in FY15. As described in the Triennial Work Project, this element of the GIS Project has defined linkages to 

other projects where a high level of GIS support would be required. Most GCMRC projects usually require 

some level of GIS support, and this usually in the form of database development, GIS layer development, and 

map outputs created for field use or for presentation and publication purposes. Below are a few more in-depth 

descriptions of GIS support provided to other science projects.

Project 3. Geomorphology: Analysis of historical images at select monitoring sites (3.1.4)

As part of the GIS project, work continued on processing Digital Terrain Models of sandabars that are 

extracted photogrammetrically from 1984 historical aerial photography. Using the new DTM extraction 

software module from ERDAS (Auto DTM), a new workflow has been created to more accurately process the 

orthophotos into 3-dimensional data sets used for determining change in sandbar volume. This new module 

includes more robust algorithms for finding similarities between stereo pair photographic frames contained 

within a photogrammetric block. Four long-term monitoring sites have been processed using this new 

software module and results are showing denser point clouds than previously generated with better accuracies 

being reported at each site. This will allow us to more accurately compare sandbar volumes between 1984 and 

when ground surveys began in the 1990s. (See Project 3, 3.1.4).
108

Project 3.5. Control Network and Survey Support: Database support and spatial analysis 

GIS staff analyzed the tabular data and fixed existing errors in survey control network database. This involved 

extracting the most recent survey control network for Grand Canyon from the existing database and importing 

it into a GIS format, developing export files for sharing data, and creating maps for field and publication use. 

Additionally, GIS staff continued the work of migrating survey control network database out of Microsoft 

Access and into ESRI Geodatabase format. This will serve as a staging repository before migrating to a 

relational database for storing, analyzing, and serving Grand Canyon survey control network data. A new 

enterprise application now exists in beta format that is designed to take survey control network data out of 

Trimble Geomatics Office (TGO), perform quality control tasks, calculate or relate additional information to 

each survey control point, and populate a new SQL database. This new database will allow for both easier 

updates to the survey control network in Grand Canyon every year and for enabling access to the survey 

control network database through a web-based interface.

Project 12 Socio-Economic Analysis: Lees Ferry Fisheries Angler Survey Analysis

The GIS project also worked with GMCRC’S Socio-Economic scientist on analyzing Lees Ferry angler 

survey data to detect spatial and temporal patterns in fisheries use data for Glen Canyon. This work involved 

processing tabular data in meaningful aggregations and building summarized spatial data sets representing 

different attributes of site visits by fishermen. These attributes including zip code information, number of 

trips, average cost of each trip, and when the trips occurred (season). From these outputs, we created a series 

of maps driven by this analysis that show spatial and temporal use patterns of the Lees Ferry fishery.

14.2 Geospatial Data Management

During FY16 the GIS project continued to serve as the Center lead for geospatial data management. This 

work involved coordinating between GCMRC science staff and the SBSC IT group to provide better support 

to science projects in the form of more reliable disk storage for data, improved communication of science 

needs to IT support staff, and an increased focus on high-level data management needs such as web server 

configurations, database server maintenance, and software installations and upgrades.

For GCMRC’s enterprise spatial database system, user-schema geodatabases in Oracle have been upgraded to 

version 10.3.1 (current ArcGIS version deployed on most machines in USGS). Also during this past fiscal 

year, the GIS project was able to expand on the scope of geospatial data hosted by the Oracle Spatial 

Database. Large, regional data sets now available through the database now include the May 2013 4-band 

overflight data, a new Glen Canyon 2013 1-meter DEM , and an updated Lake Powell 5-meter DEM and 

hillshade representing pre-dam topography.
109

During FY16, the GIS project was also involved with implementing the new USGS data review process for 

GCMRC. This work included assisting scientists with proper metadata development, review of spatial data 

characteristics (fields, values, etc.), and finalization of data review documents related to science publications.

The USGS data management protocols now require that the data used for peer-reviewed publications also go 

through a standardized review process, and be published concurrently with any publication.

14.3.1 Access to Geospatial Data Holdings – The Geospatial Portal

The GIS Project continued to advance the Center’s ability to host and share geospatial and other scientific 

data through web-based applications. This work involved testing and troubleshooting the systems (web server 

architecture, network communication, Oracle database access, and coordination with the USGS ESAS / 

Firewall team) used to serve geospatial and other data through GCMRC’s website. Upgrading these systems 

to the latest versions has provided more functionality to users of GCMRC web applications. The following is 

a descriptive list (with URLs provided) of new web-based mapping and data exploration applications now 

available through GCMRC’s website.

Improvements to the GCMRC Map and Data Portal page https://www.gcmrc.gov/dasa

The Map and Data Portal web page is the gateway to many of GCMRC’s data holdings. Available content is 

segmented according to Resource/Project type and by the nature of the content being served. This web page 

provides a more organized and modern look, and allows users to find content of interest more efficiently. This 

page also simplifies the process for adding new content to the site as it becomes available.

NEW HFE Sandbar Photo application 

https://grandcanyon.usgs.gov/gisapps/hfephotoviewer/hfe_2014.html

Available through the GCMRC Map and Data Portal are many new applications, including a revamped way 

of serving remote camera photographs that bracket the most recent HFEs from Glen Canyon Dam (2012–

2014). Additional HFE applications for past events (1996, 2004, 2008, 2012, and 2014) as well as for the 

most recent HFE in November 2016.

NEW Sandbar Time-Series Photo application 

https://grandcanyon.usgs.gov/gisapps/sandbarphotoviewer/RemoteCameraTimeSeries.html

It is also now possible to view remote camera photographs that have been subsetted to one image per day for 

the entire length of record at each site. It is strongly recommended to use the date filtering tool under Options 

in the application prior to attempting to view these photo collections as there are close to 90,000 photos 

available through this app.

UPDATED Grand Canyon GIS Portal application https://grandcanyon.usgs.gov/portal

There has been further development of the GCMRC GIS Portal to include more items, organized all web 

content on Portal into descriptive groups such as by resource type (physical, biological, socio-economic) and 

by data types (imagery, topography, base may layers, publication maps, river maps, etc.). This is a great 

platform for view basic geospatial items such as Grand Canyon map layers, river miles, imagery from past 

overflights, and topographic data sets.

UPDATED Geospatial Services page https://www.gcmrc.gov/geospatial

For GIS users, we now provide access to GCMRC’s geospatial data sets through a web services directory 

page that organizes REST service endpoints by data set and resource type. These services can be used in 

desktop applications by downloading a link (*.lyr) file of any service. They can also be accessed in web 

applications developed by users outside the GCMRC, or added into to a Google Earth session as a layer.
110

14.3.2. Access to Geospatial Data Holdings – ESRI’s ArcGIS Online 

http://usgs.maps.arcgis.com/home/search.html?q=GCMRC&t=content

We have expanded on the data made available to the public through this service. Data and services added or 

updated to ArcGIS Online include the May 2013 Colorado River Imagery, the Grand Canyon Aquatic 

Ecology Web Application, the Predicted Shorelines for High Flows application, Lake Powell Water Quality 

Station Map Service and Application, the Lake Powell Nutrient Sampling Map Service and Web Application, 

and an updated Lake Powell Pre-Dam Topography Map Service.

The benefit of using ArcGIS online in addition to hosting our own geospatial portal is that a particular service 

only needs to be created once by GIS staff, but can then be posted on both GCMRC’s website and through 

ESRI’s ArcGIS Online to reach a wider audience.

Because of the advances made in this project over the last few years, it became apparent that the lead in this 

project (GIS Coordinator) would take the initiative to begin leverage online cloud resources for delivering 

information to stakeholders and the public more efficiently in the future. This work has involved considerable 

collaboration with other IT staff in the Southwest Biological Science Center as well as with other USGS 

Science Centers.

Project 14 Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $172,900 $6,000 $16,000 $0 $0 $23,355 $218,255 

Actual

Spent $144,331 $2,430 $32,403 $0 $0 $21,469 $200,634 

(Over)/Under

Budget $28,569 $3,570 ($16,403) $0 $0 $1,886 $17,621 

FY15 

Carryover $11,090 CPI Decrease ($11,099) FY16 Carryover $17,612 

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Salary costs decreased due to vacancies.

- Operating expenses increased due to buying software.

- Carryover will be used to offset FY17 shortage.
111

FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 15: Administration

Program Manager 

(PM)

Scott VanderKooi, 

Chief

Investigator(s) (I) Scott VanderKooi, USGS 

GCMRC

Email svanderkooi@usgs.gov

Telephone 928-556-7376

SUMMARY

During the Fiscal Year 2016, this budget covered the salaries for the communications coordinator, librarian, 

and 80% of a budget analyst, as well as monetary awards for GCMRC personnel. The vehicle section covers 

the GSA vehicles that all of GCMRC use for travel and field work. The money was used for the monthly 

lease fee, mileage cost, and any costs for accidents and damages. This project also helps pay leadership 

personnel salaries, some travel and training for the Chief, and part of the salary of one program manager. This 

section also covers the costs of IT equipment for GCMRC. Logistics base cost covers salaries and 

travel/training for logistics staff.

Project 15

(- Logistics) Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $563,200 $32,000 $118,500 $81,500 $0 $87,968 $883,168 

Actual

Spent $367,175 $32,112 $114,221 $91,539 $0 $64,280 $669,327 

(Over)/Under

Budget $196,025 ($112) $4,279 ($10,039) $0 $23,688 $213,841 

FY15 

Carryover $414,395 CPI Decrease ($44,714) FY16 Carryover $583,521 

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Salary costs decreased due to GCMRC Deputy Chief and Physical Scientist vacancies.

- Cooperative agreements increased due to additional funds to NAU for support staff.

- Carryover will be used to offset FY17 shortage.
112

Logistics Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $264,500 $5,500 $793,200 $0 $0 $127,403 $1,190,603

Actual

Spent $267,490 $493 $908,270 $9,800 $0 $141,244 $1,327,298

(Over)/Under

Budget ($2,990) $5,007 ($115,070) ($9,800) $0 ($13,841) ($136,695)

FY15 

Carryover $0 CPI Decrease ($60,279) FY16 Carryover ($196,974)

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Operating expenses increased due to additional river trips and logistics expenses higher than budgeted.

- Cooperative agreements increased due to a coop. with Grand Canyon Youth.
113

FY 2016 Project Report for the Glen Canyon Dam Adaptive Management Program

Project 1: Lake Powell and Glen Canyon Dam Release Water-Quality Monitoring

Program Manager 

(PM) Scott VanderKooi Investigator(s) (I) Scott VanderKooi

Email svanderkooi@usgs.gov

Telephone 928-556-7376

SUMMARY

In fiscal year 2016, we continued to collect physical, biological, and chemical data and samples from Lake 

Powell, Glen Canyon Dam, and Lees Ferry. However, similar to FY15, we sampled less frequently and in 

fewer locations than previously due to the decision by Reclamation to begin conducting Lake Powell 

monitoring internally.

Project Summary

GCMRC has conducted a long-term water-quality monitoring program of Lake Powell and Glen Canyon Dam 

(GCD) releases. This project has been funded entirely by Reclamation from water and power revenues and 

receives no monetary support from the GCDAMP. In addition to direct funding of the program, Reclamation 

also provides support for laboratory analyses. 

The Lake Powell monitoring program was designed to determine status and trends of the water quality of 

Lake Powell and GCD releases, determine the effect of climate patterns, hydrology, and dam operations on 

reservoir hydrodynamics and the water quality of GCD releases, and provide predictions of future conditions.

Monitoring Activities

Water-quality monitoring was conducted by Reclamation from 1965 to 1996, and then by GCMRC through 

2015. For most years since 1997, the sampling program has consisted of monthly sampling in the forebay area 

immediately upstream of GCD and in the GCD tailwater, quarterly surveys of the entire reservoir, and 

continuous monitoring of GCD releases. Quarterly reservoir surveys have typically been conducted within a 

six-day time period. Monitoring has consisted of vertical depth profiles of temperature, specific conductance, 

dissolved oxygen, pH, turbidity, and chlorophyll concentrations at up to 35 locations on the reservoir, and 

sampling for major ion concentration and nutrients at a subset of these locations. In addition, biological 

samples for chlorophyll, phytoplankton, and zooplankton have been collected near the surface at selected 

stations. In FY16, Reclamation conducted two reservoir-wide surveys and GCMRC conducted four forebay 

surveys and maintained instruments monitoring GCD releases.

The beginning dates of the monthly GCMRC surveys are shown below. The surveys also included sample 

collection in Glen Canyon Dam and at Lees Ferry.

10/12/15 forebay 

01/22/16 forebay

05/31/16 forebay

07/20/16 forebay

Monitoring activities included field observations of weather conditions, Secchi depth measurements, and 

vertical depth profiling of water quality parameters. In addition, chemical and biological samples were 

collected. Analyses of these samples are usually received within two months of collection. These data are all 

entered into a Microsoft Access database. Progress continues to be made to serve data from the Access 

database on the GCMRC website.
114

Current Conditions

Hydrology - Lake Powell received 9.62 maf (89% of average) of unregulated inflow in water year (WY) 

2016, less than the inflow observed in 2015 and 2014 (94% and 96% of average, respectively), and 

significantly higher than inflows observed in 2012 and 2013 (45% and 47% of average, respectively). The 

reservoir elevation reached a peak of 3621.5 ft on July 9, 2016, compared to a peak of 3614.32 ft in 2015. At 

the end of WY2016, Lake Powell’s surface elevation was 3,610.93 ft with storage of 12.8 maf, or 53% of full 

capacity. This is similar to the end of WY2015 when surface elevation was 3,606.01 ft, and storage was 12.3 

maf.

Releases for FY16 totaled 9.0 maf (the same as for FY15) with operations under the Upper-Elevation 

Balancing Tier. Operations for FY17 will also fall under the Upper Elevation Balancing Tier, with a total 

projected annual release volume of 9.0 maf after an April 2017 adjustment. 

Glen Canyon Dam Release Temperature - Glen Canyon Dam release temperatures from 2003-2010 were 

above average because of low reservoir elevations resulting from extended drought conditions in the Upper 

Colorado River Basin. Lower reservoir elevation in 2016, combined with a relatively high inflow volume, 

also resulted in above-average release temperatures during the summer and fall of 2016, with release 

temperature nearly reaching 14°C at the end of September 2016.

Lake Powell Limnology – Similar to 2015, a winter underflow density current was not observed in spring 

2016. These density currents cause a significant freshening (i.e. increase) of hypolimnetic dissolved oxygen 

concentrations near Glen Canyon Dam. Other years when these density currents did not occur were 2006, 

2009, and 2012. The National Park Service detected larval quagga mussels in Lake Powell in the fall of 2012. 

Adult quagga mussels were discovered in Lake Powell marina areas in early 2013 and continue to increase in 

numbers.

Program Support

A five-year agreement for continued support of the Lake Powell water-quality monitoring program was 

developed with Reclamation in 2013. Funding was last received under this agreement in 2014 and all FY16 

activities were conducted using funds carried forward from this last allocation. After an internal review, 

Reclamation decided to shift Lake Powell monitoring internally. GCMRC was asked to continue conducting 

forebay sampling and water quality monitoring of GCD releases with the remaining funds from the Lake 

Powell agreement. Reclamation has expressed interest in GCMRC continuing this part of the program in the 

near term and may provide additional funding in FY17.
115

Project 1 Salaries

Travel 

& 

Training

Operating 

Expenses

Cooperative 

Agreements

To other

USGS 

Centers

Burden

Total

11.983%

Budgeted

Amount $14,295 $462 $1,266 $1,920 $17,943 

Actual

Spent $14,295 $462 $1,266 $0 $0 $1,920 $17,943 

(Over)/Under

Budget ($0) $0 ($0) $0 $0 $0 ($0)

COMMENTS (Discuss anomalies in the budget; expected changes; anticipated carryover; etc.)

- Carried $30,100 over from FY15 to FY16 and we did not receive any FY16 Funds non-AMP Lake 

Powell Funds.

- Carried over $12,200 of non-AMP Lake Powell Funds.

- Carried over $20,000 of AMP Lake Powell Funds.