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Habitat Suitability Analysis of Larval Pacific Lamprey Habitat in the Columbia River Estuary


Hoffman, Ethan; Stuart, Craig; Salazar-Velasquez, Lory; Finlay, Krista (2022), Habitat Suitability Analysis of Larval Pacific Lamprey Habitat in the Columbia River Estuary, Dryad, Dataset,


Pacific lamprey (Entosphenus tridentata) are native fish to the Columbia River Basin. Over the past 60 years,  anthropogenic disturbances have contributed to a 95% decline of historical population numbers. Member-tribes of the Columbia River Inter-Tribal Fish Commission have acknowledged the importance of Pacific lamprey to the Columbia River ecosystem and expressed concern about the loss of an essential tribal cultural resource. As a result, the Columbia River Inter-Tribal Fish Commission created the Tribal Pacific Lamprey Restoration Plan to halt their decline, re-establish the species, and restore the population to sustainable, harvestable levels throughout their historical range. 

Limited knowledge about the movement and preferred habitat of larval Pacific lamprey, such as optimal habitat conditions, demographic information, and species resilience, results in challenges to monitor and protect the species. Pacific lamprey is known to use the mainstem Columbia River to migrate between their spawning grounds and the Pacific Ocean. However, dams, levees, and culverts within the Columbia River Estuary and adjacent tributaries have restricted the lamprey’s access to spawning grounds and other upstream habitats. These restrictions have prompted conservation and restoration efforts to better understand how Pacific lamprey utilizes the Columbia River Estuary.

Here, we address these knowledge gaps in an effort to aid restoration initiatives by completing a Habitat Suitability Analysis to determine where optimal larval Pacific lamprey habitat may exist in the Columbia River Estuary. The project identified the spatial and temporal distribution of suitable habitat for larval Pacific lamprey and generated recommendations to address habitat-related knowledge gaps and further evaluate anthropogenic threats to their recovery. The results of the Habitat Suitability Analysis suggest that habitat conditions in the Columbia River itself are unable to support larval lamprey year-round, but may provide suitable habitat on a seasonal basis due to spatial and temporal limitations. However, we stress that our analyses were necessarily limited to aquatic conditions and that the temperature of the water column used in our analyses may differ from the temperature within fine sediments, where larval lamprey burrow. Our results imply that suitable lamprey habitat is present at times throughout the year in the Columbia River Estuary, and these locations can be used to support habitat restoration and conservation strategies for improving the species’ recovery. 

Anthropogenic threats to the Columbia River continue to alter habitat conditions, including average water temperature, salinity, and sedimentation. Laboratory experiments have provided insight into the potential impacts of changing temperature and salinity on larval Pacific lamprey, where elevated water temperatures can affect their development and elevated salinity levels can result in larval mortality. In addition, anthropogenic disturbances such as dams, levees, and culverts have cut off the Columbia River Estuary’s floodplain habitats from the mainstem Columbia River, decreased sedimentation rates, and separated adult lamprey from the floodplains and tributaries that they use to spawn. The presence of these barriers in the region can inhibit the distribution of fine sediments in the river, limiting where larval lamprey burrow and develop. The burrowing behavior of larval lamprey has yet to fully be investigated in the Columbia River Estuary. Limited research may be due to the lack of resources for studying Pacific lamprey’s life cycle, habitat, and population dynamics since they are not federally designated as an endangered species, like resident salmonid species. This has further added to the challenge of understanding the species and restoring its population to sustainable numbers. 

To the best of our knowledge, this project is the first to explore spatial and temporal trends of suitable larval Pacific lamprey habitat conditions in the Columbia River Estuary. The Habitat Suitability Analysis provides technical information about the presence and distribution of suitable conditions to address habitat-related uncertainties. The member-tribes of the Columbia River Inter-Tribal Fish Commission and their collaborators can incorporate the information into current and future Pacific lamprey restoration, conservation, and education programs to enhance general understanding of lamprey populations throughout the Columbia River Basin. Key recommendations are provided to address additional knowledge gaps and prioritize future restoration projects in the Columbia River Basin including the refinement of the Habitat Suitability Analysis, evaluation of barrier effects on Pacific lamprey passage, and assessment of climate change scenarios on larval lamprey habitat.


The Habitat Suitability Analysis uses salinity, temperature, and geomorphology data to identify suitable larval Pacific lamprey habitat in the Columbia River Estuary. In addition, the analysis uses hydrogeomorphic reach data of the Columbia River Estuary. The monthly salinity and temperature data was obtained from a Oregon Health & Science University's Center for Coastal Margin Observation & Prediction hindcast simulation database known as db33. This simulation's outputs were projections that were based on 20-year averages between 1999 and 2018 and resulted in daily summary statistic files; these files were binned by month to produce GeoTIFF files, consisting of 12 individual raster files for each month. In total, there are 12 salinity GeoTIFFs (units are in Practical Salinity Units, which are roughly equivalent to Parts Per Thousnd) and 12 temperature GeoTIFFs (units are in degrees Celsius). Each GeoTIFF summarized salinity or temperature conditions for that month of the year. For example, one raster file contains the summary statistics for all Aprils between 1999 and 2018.

The geomorphology data and hydrogeomorphic reach data are layers from a Columbia River Estuary Ecosystem Classification geodatabase from the Lower Columbia Estuary Partnership's website. The geomorphology data (also known as geomorphic catena) is a vector layer that contains individual landforms within the Columbia River's ecosystem complexes that were created over the past 2,000 years. Examples include natural levees, bedrock, and floodplains. The hydrogeomorphic reach data is a vector layer that divides the Columbia River Estuary into eight separate regions based on the region's biophysical characteristics.

This dataset also uses a shapefile layer of the Columbia River Basin called "Columbia Basin Streams" to define the research project's region of study. This shapefile layer was obtained from NOAA Fisheries' Columbia Basin Historical Ecology Project Data, though it was replaced by the hydrogeomorphic reach data during the analysis process

All of the datasets were processed using the ArcGIS Pro 2.6.0 ModelBuilder by using a binary classification system to reclassify the salinity, temperature, and geomorphology data. This project had researched environmental parameters that were critical for larval Pacific lamprey survival and identified specific salinity and temperature ranges using scientific literature. Salinity and temperature values that fell within their respective ranges were assigned a 1, while salinity and temperature values that did not fall within the range were assigned a 0. This process was completed for each month of the year. The geomorphology data was assigned a binary classification based on whether the habitat within the layer was predominantly aquatic; layers that were predominantly aquatic would be suitable for larval Pacific lamprey were assigned a 1 while layers that were not predominantly aquatic would be unsuitable for larval Pacific lamprey and were assigned a 0. The researchers then used ArcGIS Pro's Raster Calculator tool to sum the reclassified output for each month, and then multiplying the monthly salinity results by the monthly temperature results and the geomorphic catena results. This resulted in 12 outputs per month where suitable habitat was either met or not met. The last step of the Habitat Suitability Analysis combined the resulting 12 output layers of monthly suitable habitat into a single Raster Calculator to add the number of months where suitable habitat was met.

Usage Notes

The Habitat Suitability Analysis was built using ArcGIS Pro's ModelBuilder tool. This program does not have an option to save the model's inputs as a relative file path. As a result, the model may not run because it's searching for each layer's original file path. If this happens, we have included a file titled Habitat_Suitability_Analysis_Script that outlines the processes we used to build the model.

This submission contains three folders and three supplemental files. The folder titled "Data" includes all of the raw data and data input in the Habitat Suitability Analysis. The folder titled "Scripts" describes the steps to build the Habitat Suitability Analysis model in ArcGIS Pro. The Results folder contains the Habitat Suitability Analysis model and the data that was input into the model. The supplemental files are a file titled "Dryad_Folder_Contents" which describes the contents of every folder in this submission, and a file titled "Habitat_Suitability_Analysis_README" which contains information about the Habitat Suitability Analysis dataset and sources for the data used in the analysis, and a file entitled "Lamprey_League_Final_Report" describes how the Habitat Suitability Analysis was used to identify suitable larval lamprey habitat.


DiPaola Foundation