DOI: 10.25349/d98d05
title: Habitat Suitability Analysis of Larval Pacific Lamprey Habitat in the Columbia River Estuary

description: 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.
description: 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.
description: 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.