DOI: 10.5061/dryad.xksn02vpx
title: Facilitated migration could bolster migrant passage through anthropogenically altered ecosystems

description: 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.
description: # Facilitated migration could bolster migrant passage through
 anthropogenically altered ecosystems
 [https://doi.org/10.5061/dryad.xksn02vpx](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](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](https://doi.org/10.6073/pasta/3534f98e531d7238dca001bfd8e55dcf). USGS (2024). USGS Water Data for California. [https://nwis.waterdata.usgs.gov/ca/nwis](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.