10.25349/D98D05
Hoffman, Ethan
0000-0002-4746-3606
University of California, Santa Barbara
Stuart, Craig
University of California, Santa Barbara
Salazar-Velasquez, Lory
University of California, Santa Barbara
Finlay, Krista
University of California, Santa Barbara
Habitat Suitability Analysis of Larval Pacific Lamprey Habitat in the
Columbia River Estuary
Dryad
dataset
2022
FOS: Earth and related environmental sciences
Entosphenus tridentatus
Pacific Lamprey
Columbia River Estuary
Habitat Suitability Analysis
ArcGIS Pro
ArcGIS Pro 2.6.0
ArcGIS Pro ModelBuilder
Columbia River
DiPaola Foundation*
University of California, Santa Barbara
2022-05-31T00:00:00Z
2022-05-31T00:00:00Z
en
https://bren.ucsb.edu/projects/identification-and-conservation-larval-pacific-lamprey-habitat-columbia-river-estuary
https://doi.org/10.5281/zenodo.6525884
https://doi.org/10.5281/zenodo.6525886
1276101520 bytes
3
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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.