GEOG 566

         Advanced spatial statistics and GIScience

April 6, 2019

Monitoring Stage 0 Restoration Effects on the South Fork McKenzie River

Filed under: 2019,My Spatial Problem @ 3:35 pm

Research Question

How is the spatial presence of aquatic organisms in the lower South Fork McKenzie River related to the spatial presence of hydromorphological changes induced by Stage 0 stream restoration?

Global hydrologic systems historically contained anastomosing (braided and connected) channels and active floodplains. Anthropogenic disturbances of the late 19th and early 20th centuries and prevailing natural disturbances are responsible for the channelization and incision of stream systems worldwide. Stage 0 riparian restoration restores degraded streams to historic conditions through large woody debris placement and filling in channels to increase aquatic habitat quality and availability. In this study, I will explore Stage 0 restoration effects on a 2 mile reach of the lower South Fork McKenzie River 45 miles east of Eugene, OR. I will test these effects by spatially relating early post-restoration species colonization to restoration-induced hydromorphological changes. These morphological changes include habitat features created by the reduction and redirection of water flow energy, such as riffles, pools, side channels, slack water, and sediment and organic material deposition. Aquatic organisms depend on these features for critical habitat. Therefore, sampling for aquatic species presence before and after restoration will indicate how successful Stage 0 restoration was in creating habitat features for these organisms.


I will analyze two biological datasets to detect species presence and multiple remote sensing datasets to detect hydromorphological features. The first biological dataset includes pre- and post-restoration lentic (still freshwater) and lotic (rapid freshwater) aquatic macroinvertebrate samples taken at established transects and randomly throughout the study area. The second biological dataset includes eDNA samples taken at these same transects, intended to capture up to 48 species in a single sample (macroinvertebrates, fish, amphibians, crayfish). The remote sensing datasets include pre- and post-restoration aerial lidar, bathymetric lidar, Structure from Motion, RGB, multispectral, and thermal infrared products acquired with an Unmanned Aerial System for the 2 mile reach. The temporal resolution for all datasets are approximately 1 year (summer 2018 – summer 2019). The datasets are collected pre- and post-implementation (summer 2018) in the early summer during high flow conditions and early fall for low flow conditions. The spatial resolution of the UAS datasets is fine scale (sub-meter to cm).


In the biological datasets, I expect to see macroinvertebrate presence clustered around features characterized by low velocity, shallow depth, and high organic material. These features allow macroinvertebrates foraging ease and shelter from predators. I expect species type to be dominated by post-disturbance colonizers throughout the system. I expect the eDNA data to return descriptions of upstream-downstream species presence. I expect non-macroinvertebrate species to be present in areas with more pools, side channels, and high wetted area, which provide habitat for resting, feeding, and nurseries. I expect the macroinvertebrate eDNA data to reflect the physical sampling data. In the remote sensing datasets, I expect habitat features to be present downstream of and adjacent to large woody debris, sediment deposits, and organic material, since these factors reduce and redirect flow energy for establishment of lentic and lotic features (e.g. pools, riffles, slack water).


All analyses will consider pre- and post-restoration variables to determine rate and degree of change. I would like to learn about spatial autocorrelation analyses such as Moran’s I. It is likely that in these datasets I will find patterns of dependent observations based on localized conditions. For example, aquatic species presence may be grouped according to centralized nursery or hatch locations, so they are not truly independent samples. Fish species presence may be grouped based on macroinvertebrate presence as a food source, and certain species may be grouped by areas of similar substrate sizes. Regression analyses showing relationship strengths between different combinations of species and morphology variables (such as PCA) could indicate the likelihood of certain features affecting species colonization.

Expected Outcome

I will produce site maps showing point and polygon locations of certain hydrologic features alongside point locations of specific aquatic species presences and types. For the eDNA datasets, I will produce graphs indicating the presence and type of species detected. Ideally, I will be able to determine correlation coefficients for the relationships between specific hydrologic features created and the presence and location of aquatic species types, likely presenting them in a correlation matrix.


 This research presents a novel opportunity to study Stage 0 restoration. Powers et al. (2018) present one of the only formal studies investigating Stage 0 restoration outcomes. This study will add to the limited knowledge surrounding this relatively unexamined strategy. To my knowledge, this proposal will be the first study testing Stage 0 UAS monitoring and one of the few existing studies linking aquatic organism sampling to UAS hydromorphology datasets. On a regional scale, U.S. Forest Service fisheries and hydrology divisions in the Pacific Northwest and across the United States will design restoration effectiveness monitoring objectives using results from this study. The McKenzie Watershed Council will determine their implementation techniques and success rates on future projects with results from this study. The study results will provide a viable Stage 0 restoration monitoring methodology for agencies and landowners on a global scale. The South Fork McKenzie River also sustains fish species listed as Endangered and Threatened under the Endangered Species Act, specifically the Chinook salmon (Onchoryncus tshawytscha) and bull trout (Salvelinus confluentus), respectively (USFWS 2019). These species use the South Fork McKenzie River for annual spawning and rearing habitat and feed on resident macroinvertebrates (Meyer et al. 2016). The Chinook salmon and bull trout are among the western U.S.’s most controversial game fish due to the environmental policies surrounding their protection. Conflicts among agencies, companies, and the public frequently arise concerning these species’ conservation. Researching restoration effects on Chinook salmon and bull trout habitat and food sources will provide scientific basis for management decisions regarding these fish.

Level of Preparation

I took an Arc-Info (ARC Macro Language) class during my undergraduate program. I am currently taking a Python class for geospatial programming, which is my only experience with this language. I have experience in image processing through an undergraduate degree in land use and GIS, multiple years of professional experience in remote sensing and GIS, and my current MS program in Forest Geomatics. I have academic and professional experience with R, C++, ArcGIS, and multiple types of remote sensing software for 2D and 3D analysis.


Meyer, K., Hammons, B., Hogervorst, J., Powers, P., Weybright, J., Bair, B., Robertson, G., Mazullo, C. (2016). Lower South Fork McKenzie River Floodplain Enhancement Project 80% Design Report. Prepared by the Willammette National Forest and McKenzie Watershed Council, March 4, 2016.

Meyer K. (2018). Deer Creek: Stage 0 alluvial valley restoration in the western Cascades of Oregon. In StreamNotes: The Technical Newsletter of the National Stream and Aquatic Ecology Center, David Levinson (editor). US FOrest Service, Fort Collins, CO, May 2018.‐05.pdf

Newson, M.D., Newson, C.L. (2000). Geomorphology, ecology and river channel habitat: mesoscale approaches to basin-scale challenges. Progress in Physical Geography 24(2), 195 – 217.

Powers, P. D., Helstab, M., & Niezgoda, S. L. (2019). A process-based approach to restoring depositional river valleys to Stage 0, an anastomosing channel network. River Research and Applications, 35(1), 3–13.

U.S. Fish and Wildlife Service. (2019). Environmental Conservation Online System.

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1 Comment »

  1.   jonesju — April 7, 2019 @ 2:19 pm    

    Katie, excellent start. I take it your study site is the S Fork McKenzie downstream of Cougar Dam? I encourage you to read the MS thesis of Stephanie Bianco about stage 0 restoration on Deer Creek, For your analyses, consider the following. For Ex. 1, try testing for spatial pattern and/or spatial autocorrelation in at leastone of the biological datasets, and also in one of the physical habitat variables (such as pool depth). You may also wish to try to interpolate observations to create maps. For Ex 2, use cross-correlation or GWR to test for spatial relationships.

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