# Presentation: 322604

## The Research, Monitoring, and Evaluation program in the John Day Basin; a hierarchical framework Nick BouwesEco Logical Research, Logan UTMichael NewsomBureau of Reclamation, Portland ORChris JordanNorthwest Fisheries Science Center, Seattle WA

**Notes:**
As you know there is a Biological Opinion authored by NOAAF describing how we must mitigate for the impacts of the mainstem Snake and Columbia River dams on salmon and steelhead listed under the ESA.  Part of the mitigation, to make up for these impacts, is to improve spawning and rearing habitat in the tributaries.  Part of this BiOp calls for the development of a research, monitoring, and evaluation program throughout the Columbia River basin referred to as the Federal RME program.  This program will be used to describe the status and trends of these fishes and their habitat, identify mitigation opportunities, and evaluate the response to mitigation actions. 

## Why use the John Day as a pilot subbasin for the Federal RME program?

**opportunity to use past research to develop mitigation strategies (temperature, water supply, sediment)**
**little influence of hatchery fish**
**information may be transferable to other ESUs **

**Notes:**
Although there are several RME efforts throughout the CRB, there is little communication between them and each with different goals.  The FRME goal is to implement an RME program throughout the CRB that is somewhat standardized between subbasins, designed in such a way as to address multiple information goals. Development of a comprehensive RME program will be a learning process, and thus going through the trials and errors at the scale of the Columbia River Basin would be impractical.  Therefore, it was agreed that development of a CRB RME program will occur three Pilot subbasins, the Wenatchee, Salmon, and John Day Basins.

The John Day has been chosen as a pilot subbasin within the Columbia River Basin because 6 of 12 steelhead populations of the mid-Columbia ESU reside in the JDA,  a wealth of research and background knowledge exist that will be useful in developing experimental mitigation strategies.  There are no hatcheries in the JDA to complicate matters although current info is suggesting that strays are found there. Also because the RME efforts in these 3 basins cover a large range of conditions, the information likely brackets other environmental conditions of other ESUs.   

## Analytical Framework Group

**forum to discuss research and monitoring strategies and needs**
**ensure continuity between different projects**
**reduce duplication of efforts, increase cooperation**
**integrate research and monitoring results**
**develop appropriate mitigation experiments **

**Notes:**
Design of F RME in the JDA is occurring mainly through the Analytical Framework group.  Members of this workgroup represent several federal and state agencies and in have a background in the JDA useful in fast-track development of mitigation efforts.  This AFG is a way in which we can discuss RME strategies and needs....

shared labor

## AFG and other workgroups in the John Day

**Analytical Framework **
**Group**

**Freshwater Production**
**Group**

**Habitat Monitoring **
**Group**

**Geodatabase Design**
**Group **

**Notes:**
Other workgroups have been discuss habitat and fish monitoring design and protocols for status and trends and eventually effectiveness monitoring.  Also another effort is underway to develop a geo referenced data base flexible enough to incorporate information from all monitoring programs. In addition, a data dictionary- or definitions of the protocols used in the monitoring programs, is part of this effort.  Overlap in membership between the different workgroup ensures some continuity.   

## Implementing restoration while maximizing learning

**State Overall**
** ****Goals**

**evaluate**
**results**

**link results to**
**decision**

**experimental **
**management**
** ****design**

**implement**
**action**

**implementation**
**& effectiveness**
** ****monitoring,**
**research**

**identify**
**the problem,**
**establish**
** ****baseline**

**status & trend**
**monitoring,**
**research**

**synthesize**
**exploratory**
**information**

**refine **
**questions**
**into**
**hypotheses**

**Notes:**
A goal of the BiOp, of which the RME program will inform, is identification, implementation, measurement of responses of effective mitigation strategies. These are the steps we believe are necessary to design effective mitigation strategies while maximizing learning, in other words developing an experimental management approach.  
First step is state your goals as concisely as possible.  Your goal could be, for example, to increase the population of an ESU.  Alternatively you could be more precise, increase freshwater production of the John Day populations by 10%.  This focuses your research.  Goals will like be refined. 
Next, it is important to identify the problem.  What is it you are trying to fix.  Most restoration efforts fail because they have not identified the problem, they just apply a package restoration. May be ineffective and expensive.  In addition, efforts should be made to describe a baseline or current condition in which to describe status and trends and to compare to post mitigation response.    
This will require status and trends monitoring of fish and habitat, and research directed to understand mechanisms responsible for limiting salmonid production.  Monitoring coupled with research greatly increase the power in which to make inferences.  This information has to be synthesized to identify the problem and to refine broad questions into testable hypotheses.  Likely, iterative approach.  Hypotheses should be much more specific than goals (i.e. the presence of fine sediments reduces the amount of available spawning habitat, or temperatures are above optimal to maximize growth in juvenile steelhead).
So we design an experiment to test this hypothesis. This includes design of effectiveness monitoring, and directed research to document mechanisms of the response. We implement the restoration action and measure the response over time. We evaluate the results, and use this information to make decisions about further actions.  This may alter our view of original goals. 
Developing an RME program for a localized experimental management project, will test the ability of the program to meet the needs of large scale restoration efforts.  

## Implement restoration and maximizing learning

**State Overall**
** ****Goals**

**evaluate**
**results**

**link results to**
**decision**

**experimental **
**management**
** ****design**

**implement**
**action**

**implementation**
**& effectiveness**
** ****monitoring,**
**research**

**identify**
**problem,**
**establish**
** ****baseline**

**status & trend**
**monitoring,**
**research**

**synthesize**
**exploratory**
**information**

**refine **
**questions**
**into**
**hypotheses**

**Notes:**
Currently, research and monitoring coordinated the AFG is more exploratory in nature.  This includes 2-5 yrs worth of information which have just started to try to synthesize.  I will describe some of the efforts in a minute.  The goal ahead of us is use this synthesized information to come up with specific hypotheses to develop an experimental restoration project.  We are hoping to implement this by 2005 field season.

## spatial scale

***spatial scale***
***(m)***

**basin**
**(*****John Day*****)**

**subbasin**
**(*****Middle Fork***** *****John Day*****)**

**watershed**
**(*****Long Creek*****)**

**reach**
**(*****1 km of Long Creek*****)**

**monitoring and experimental sites**

**Scale Hierarchy**

**Biological Hierarchy**

**population**
**(*****John Day spring Chinook*****)**

**sub-population**
**(MF *****John Day spring Chinook*****)**

**local groups**

**small groups**
**or**
**individuals**

***10******5******-10******6***

***10******2******-10******4***

***10******0******-10******1***

**Notes:**
The AFG has organized research to address questions in hierarchical fashion across multiple scales. 
In the JDA, research has been developed to address landscape/landuse patterns relative to the distribution of the John Day salmon and steelhead populations. This provides the context to view watershed/reach scale habitat information and fish subpopulations – maybe most relevant to a salmonids needs through a majority of the life history.  Understanding the mechanisms by which physical and biological interactions likely will occur at smaller scales and directed research.   As some of you may recall this is similar to the level of organization of the F RME program, with Tier 1 through 3 questions.

The goal is to not only describe interactions between physical and biological properties within a level but also between level, thus the hierarchical design.

## Basin

**push-up dams**

**behavior**

**growth**

**survival**

**production**

**TMDL**
- (ODEQ)

**Push-up Dam Removal Project **(OSU)

**temperature**

**GIS Database**
- (GIS Group)

**basin,**
**subbasin:**
**landscape **
**land use**

**watershed,**
**reach:**
**land use habitat**

**Freshwater Production **(ODFW)

**Spawning Ground Surveys**
- (ODFW)

**habitat reference sites**

**Habitat Monitoring Group**
- (USFS, ODFW, ODEQ)

**Juvenile Monitoring (**ODFW)

***Basin***

***Site***

**Fine Sediments**

**Fine Sediment Analysis **(EPA)

**Juvenile Salmon and Steelhead Production Project **(OSU)

**Channel Incision**

**Channel Incision project**

**Spatial Data Analysis**
- (OSU)

**Landscape Change and Patterns**** **(NOAAF)

**Notes:**
This diagram will attempt to illustrate how the research and monitoring has been organized by the AFG to address questions at multiple scales. Topics of study will be arrange roughly as large scale on the left to finer scales as we move to the right.  I will illustrate how one thread of studies may address factors influencing stream temperatures which can influence salmonid production. 
At the basin/subbasin scale we are addressing landuse/landscape temporal and spatial pattern’s ability to describe habitat patterns at the watershed/reach scale.  The spatial data analysis study is conducting LIDAR and FLIR remote sensing and relating this to habitat patterns at the reach scale. 
 If we zoom in on watershed/reach level we have studies describing how habitat impacts specific reach features, in this case temperature.  A TMDL model will make crucial connections between reach scale habitat features and instream heat budgets. OSU studies are looking at how temperature impacts fish behavior (movement), growth, survival, and ultimately production.  
Now there also several habitat monitoring programs in the region as well as fish monitoring programs. All of this information will eventually be house in the GIS database.  
In actuality, there are several other studies in place to look other factors such as sediment impacts and channel incision problems. I would be happy to chat about this fascinating research when time is not a constraint.
This is a quick description of the exploratory research underway.  

## Implement restoration and maximizing learning

**State Overall**
** ****Goals**

**evaluate**
**results**

**link results to**
**decision**

**experimental **
**management**
** ****design**

**implement**
**action**

**implementation**
**& effectiveness**
** ****monitoring,**
**research**

**identify**
**problem,**
**establish**
** ****baseline**

**status & trend**
**monitoring,**
**research**

**synthesize**
**exploratory**
**information**

**refine **
**questions**
**into**
**hypotheses**

**Notes:**
This exploratory information will be crucial in the design of an experimental restoration project, the second half of this diagram that I will describe next.   

## Identifying mitigation strategies and their responses in the John Day Basin: 

**  ****What are the steps necessary in developing and implementing an experimental restoration program for a  given watershed?  **
**	****Intensively Monitored Watershed study**
** **** ****What are the steps necessary in developing and prioritizing mitigation efforts by watershed at scale of the John Day Basin?**
**      ****Watershed Assessments**

**Identifying mitigation strategies and their responses in the John Day Basin: **
**Two parallel processes**

**Notes:**
We will attempt to lay out a process by which mitigation strategies in the John Day Basin will be identified, implemented, and their responses monitored.  To do this we will operate at two different scales.  First we will operate a watershed scale and ask the question: What are the steps necessary in developing and implementing an experimental restoration program in a given watershed? We refer to this as the Intensively Monitored Watershed study.  

Second, we will ask: What are the steps necessary in developing and prioritizing mitigation efforts, by watershed at scale, of the John Day Basin?  This will initially be a large scale watershed assessment.

## Identifying mitigation strategies and their responses in the John Day Basin: Intensively Monitored Watershed study

**Define hypothesis to test**
**Experimental manipulation of identified limiting ****	****factors**
**experimental design (e.g. BACI)**
**monitoring design**
**Implement restoration in the treatment watershed**
**Monitoring and research to detect imposed changes**
**Analysis of results**
**Synthesis of results to inform decision making**

**Identifying mitigation strategies and their responses in the John Day Basin:** Intensively Monitored Watershed study

**Notes:**
As I mentioned previously, we are implementing the “ideal” experimental management action within a given watershed as a means of testing the process of: identifying the problem, including understanding the mechanisms limiting fish production and the landscape context for these interactions, establishment of status and trends of fish and their environment- These steps are the exploratory investigations I just desribed; we must now define specific hypotheses to test when implementing a watershed restoration program and designthe experimental manipulation that achieves restoration goals while maximizing learning.  
This includes: experimental design, such as BACI design, where before and after comparisons are made between trt and control watersheds; research to determine whether mechanisms responsible for changes are as expected (or even more interesting if responses are unexpected); and effectiveness monitoring of a priori responses, so protocols, sample design, sample sizes of expected effects sizes are determined. 
We then implement the identified restoration activity. Overcoming the logistical challenges of this will be part of the learning process. 

And then we go through the steps of measuring the responses synthesizing the results and making a decision about the effectiveness.

## Example experimental watershed design

**Notes:**
For example, a fair amount of research and monitoring has been conducted in the SF of the John in different watersheds.  Name them.  Much of this has been conducted by researchers and graduate students at OSU.  This includes GIS studies, remote sensing, habitat monitoring, and fish monitoring and research.  

## Example experimental watershed design

**Notes:**
Fish have been PIT-tagged throughout the SF watersheds.  

## Example experimental watershed design

**Notes:**
Ian Tattam, a grad student at OSU, has set up PIT-tag antennas and ODFW has been operating the screw traps.  Using mark-recapture techniques, survival of juvenile steelhead can be estimated through detections at the antenna, screw traps and Mainstem dams on the Columbia.  Survival, growth, behavior can be related to the habitat conditions in which juv stlhd were observed.   

This information will lead insight into mechanisms limiting production and status and trend information that will form a baseline.  

## Example experimental watershed design

**Notes:**
An example of experiment may be to fence sections of say Murderers Creek, where there currently is grazing,  and use other watersheds as controls, and continue this research and monitoring while added more monitoring of expected response. 

## Identifying mitigation strategies and their responses in the John Day Basin: Watershed Assessments

**Limiting factors of watersheds - Subbasin planning, EDT,  TRT products,  watershed and recovery plans **
**Prioritization of restoration efforts - assess potential ****	****importance for restoration defined as:**
**Historic to Current (inherent potential of WS)**
**Practicality (can the work be done)**
**Likelihood to detect change**

- Identifying mitigation strategies and their responses in the John Day Basin: Watershed Assessments

**Notes:**
However, we need to do this at the scale of the JDA. While this will be much more difficult, we can make progress on this while implementing an IMW.  Our plan is to conduct watershed assessments.  First by describing how they fit into the observed landscape patterns and land use practices.  A limiting factors analysis will have to be conducted for the various watersheds.  This is where we can tie in other efforts that have been working towards this goal such as subbasin planning which has used the Ecosystem Diagnositic and Treatment model to begin to look at this.  Other processes will also feed into this larger effort such as the TRT, and watershed and recovery plans.
Next, we will prioritize restoration efforts defined as potential, practicality (e.g. private landowners, expense, etc.) and the likelihood to detect change given what we learned for the ability of monitoring programs distinguish signals from noise.   These steps are largely exploratory in nature. 
Multiple restoration project throughout the JDA will likely be done in cooperation of several interested parties. Lessons learned in the IMW study will be useful in setting these projects in an experimental management approach and developing RME programs to determine benefits from these activities. The larger scale of the John Day may provide opportunities for greater spatial comparisons, higher replicates of trts, and controls, and greater universe of restoration types.  There may also be opportunities to evaluate existing restoration activities retrospectively.  

## Summary of progress of the John Day RME pilot project

** ****Establishment of an Analytical Framework****- **
**	****2004 AFG document**
** ****Implementation of complementary research projects ****	****across multiples scales**
** ****Completion of 1-2 seasons of exploratory research ****	****including: GIS analyses, LiDAR, FLIR remote ****	****sensing, TMDL models, fish behavior, growth, and ****	****survival**

## Summary of progress of the John Day RME pilot project

** ****Conceptualization of how to identify mitigations  strategies and their responses **
** ****Intensively monitored watershed study **
** ****Watershed assessments**** **