Facilitated migration could bolster migrant passage through anthropogenically altered ecosystems
Data files
May 24, 2024 version files 4.46 MB
Abstract
Anthropogenic habitat change frequently outpaces the adaptive capacity of migratory taxa, placing many species and populations at risk of extirpation or extinction due to the mismatch of natural migration phenology and suitable conditions. While dynamic protection can greatly benefit migratory species, it is contingent on the flexibility of relevant management actions. For regulated ecosystems where advanced management planning is required, we present a framework—facilitated migration—for actively matching natural migration phenology with suitable conditions for successful migrant passage. Using a case study of juvenile Chinook salmon (Oncorhynchus tshawytscha) oceanward migration in the Sacramento River, a major bottleneck to the recovery of imperiled populations in California, we show how the conditions associated with migration preparation, migration initiation, and successful migrant passage could be regulated to benefit migrants. Thermally shifted preparation, flow pulse-mediated initiation, and passage protection via increased flow, all accomplished by controlling the release of water from storage reservoirs, could increase the number of wild-origin Chinook salmon populations successfully migrating to the ocean by at least 18-212% compared to the status quo management scenario. To further inform expected outcomes, we find that the temporal scope and diversity of juvenile salmon lifestages studied via acoustic telemetry should be expanded, and that the range of flows and flow changes that juvenile salmon experience should be increased. Facilitated migration works by synchronizing migration—thus, a prudent course of action when implementing this strategy would be to favor event quality over event quantity. In forcing scientists and managers to critically evaluate how migrations can be supported and manipulated, facilitated migration will help migratory species persist in anthropogenically altered ecosystems.
README: Facilitated migration could bolster migrant passage through anthropogenically altered ecosystems
https://doi.org/10.5061/dryad.xksn02vpx
Brief summary
Data products were derived from three raw data sources: Interagency Telemetry Advisory Group (ITAG) Central Valley Enhanced Acoustic Tagging Project (ITAG 2024), US Fish and Wildlife Service (USFWS) Red Bluff Diversion Dam (RBDD) Rotary Screw Trap (RST) Juvenile Fish Monitoring Database (Voss 2024), and US Geological Survey (USGS) Water Data for California (USGS 2024). These data products are intended for use with the accompanying R code.
References
ITAG (2024). Central Valley Enhanced Acoustic Tagging Project. https://oceanview.pfeg.noaa.gov/erddap/tabledap/FED_JSATS_detects.html
Voss, S. (2024). USFWS Red Bluff Diversion Dam Rotary Screw Trap Juvenile Fish Monitoring Database v10. Environmental Data Initiative. https://doi.org/10.6073/pasta/3534f98e531d7238dca001bfd8e55dcf.
USGS (2024). USGS Water Data for California. https://nwis.waterdata.usgs.gov/ca/nwis
Description of derived data products
migration_R1_data.csv
Data for use with passage_R1.R, preparation_R1.R, and efficacy_R1.R. Each line represents a RBDD RST sampling event that attempted to catch wild-origin juvenile Chinook salmon fry or smolt lifestages. Data are in long format such that each unique sampling event is represented by 4 rows: one datum for each run (fall, late fall, winter, or spring). Date, or the date of sampling, is the unique identifier that links each sampling event with raw data (Voss 2024). water_year_n is the water year of the Date, water_year_doy is the day of the water year of the Date, and common_doy is water_year_doy standardized to the day of minimum passage for each run so that all studied populations were on the same scale. run (fall, late fall, winter, or spring) defined the studied salmon populations. fry and smolt are the number of each lifestage caught in a given sampling event, and passage is the combined total of the two lifestages.
passage_R1_data.csv
Data for use with passage_R1.R and efficacy_R1.R. Each line represents an acoustically tagged juvenile Chinook salmon smolt that attempted to migrate through the Sacramento River watershed to the Pacific Ocean. fish_id is a unique identifier that links each acoustically tagged fish with raw data (ITAG 2024). release_latitude and release_longitude describe locations where tagged fish were released in the Sacramento River watershed. release_river_km is the river kilometers from release location to the Pacific Ocean, or the migration distance. mid_mig_date is the date and time of the midpoint of migration, and water_year_doy is that date in terms of the water year. temp_c is temperature (°C) (USGS 2024), flow_cms is river flow (m3s-1) (USGS 2024), cond is fish condition factor (100 x g x cm-3), origin is hatch (hatchery) or wild, and survival is whether (1) or not (0) the migration was successful.
preparation_R1_data.csv
Data for use with preparation_R1.R and efficacy_R1.R. Each line is a unique RBDD RST sampling event that yielded a 10% threshold for each population during a given water year. Date, or the date of sampling, is the unique identifier that links each sampling event with raw data (Voss 2024). run (fall, late fall, winter, or spring) and lifestage (fry or smolt) defined the studied populations. water_year_doy is the day of the water year corresponding to Date, water_year_doy_n is water_year_doy + the number of days in the water year for populations that straddled water years, and common_doy is the date of 10% passage standardized to the date of minimum passage for each run so that all studied populations were on the same scale for modeling. temp_15, temp_30, temp_45, and temp_60 respectively represent the average daily temperature (°C) for 15, 30, 45, and 60 days (USGS 2024) leading up to the 10% threshold. dis_15, dis_30, dis_45, and dis_60 respectively represent the daily average flow for 15, 30, 45, and 60 days (USGS 2024) leading up to the 10% threshold.
initiation_R1_data.csv
Data for use with initiation_R1.R and efficacy_R1.R. Each line is a unique RBDD RST sampling event. Date, or the date of sampling, is the unique identifier that links each sampling event with raw data (Voss 2024). water_year_doy is the day of the water year corresponding to Date, and year is the water year in character format. flow_last_week and flow_diff_day_before_week are baseline flow and flow change corresponding to a given Date (USGS 2024). tot_smolt is the total number of smolts caught, and tot_smolt_log is that number log-transformed. Similarly, tot_fry is the number of fry caught, and tot_fry_log is that number log-transformed.
Description of R code
scenarios_R1.R
R code that produces Figure 2. No input data.
passage_R1.R
R code that uses passage_R1_data.csv and migration_R1_data.csv as inputs. Produces Figure 3, Figure 4, Figure 5, Figure S1, Figure S2, Figure S6, and Figure S7.
preparation_R1.R
R code that uses migration_R1_data.csv and preparation_R1_data.csv as inputs. Produces Figure 6, Figure S3, and Table S1.
initiation_R1.R
R code that uses initiation_R1_data.csv as the input. Produces Figure 7, Figure S4, Figure S5, Figure S8, and Table S2.
efficacy_R1.R
R code that uses all derived data products as inputs. Produces Figure 8.