DOI: 10.5061/dryad.7sqv9s521
title: Data from : Variation in salmon migration phenology bolsters population stability but is threatened by drought

description: Intrapopulation variation in movement is common in nature but its effects
 on population dynamics are poorly understood. Using movement data from
 3,270 individually-marked fish representing nine cohorts of coho salmon
 (Oncorhynchus kisutch) in California, we show that bimodal intrapopulation
 variation in the timing of juvenile down-migration from their natal
 habitat and subsequent residence in non-natal habitat affects growth,
 emigration timing, and the abundance and stability of adult returns.
 Non-natal rearers (early down-migrants) exhibited more variable growth and
 more variable but earlier emigration to the estuary than natal rearers
 (late down-migrants). While natal rearing was more common, non-natal
 rearers were overrepresented among adult returns, and non-natal returns
 were 1.6 times more stable than natal returns. Our results demonstrate
 that variation in migratory behavior bolsters population stability through
 portfolio effects. However, non-natal rearing is reduced in low water
 years, suggesting that drought exacerbates population instability by
 reducing critical intrapopulation variation.
description: # Data for: Variation in salmon migration phenology bolsters population
 stability but is threatened by drought.
 [https://doi.org/10.5061/dryad.7sqv9s521](https://doi.org/10.5061/dryad.7sqv9s521) **Description of data and file structure** These data are associated with analyses for the submitted manuscript entitled "Variation in salmon migration phenology bolsters population stability but is threatened by drought." The submission includes six data files: * "willow.MS1.share.csv" includes all data on coho salmon released into Willow Creek from the Don Claussen Fish Hatchery that were subsequently detected at both the upper and lower PIT antennas. These data were downloaded from a Sonoma Water (SW) database on November 13, 2023. * "AdultPITNumbers.csv" contains the PIT tag numbers and associated metadata for fish detected by the SW and California Sea Grant (CSG) monitoring in the Russian River that were identified as adult returns by CSG and SW staff. * "WIL-antenna-efficiency.csv" contains the estimated detection efficiencies for each site and season. For additional details on efficiency calculations see Horton et al. 2011. * "dsmt_prop.csv" count data from the downstream migrant trap by origin (hatchery vs. wild) * "releases.csv" includes the number of hatchery fish released each hatch year (including both tagged and untagged fish) * "wild.csv" includes the tagging and detection records for wild fish tagged during electrofishing surveys For details on data collection, see the [California Sea Grant website](https://caseagrant.ucsd.edu/russian-river-salmon-steelhead]) and reports therein. The submission also includes one code file in the form of RMarkdown "Willow_MS1.R" which contains all analyses associated with the manuscript ## Description of the data * "willow.MS1.share.csv": * PITNumber: factor; The unique code identifying individual fish that is the tag number from the implanted Passive Integrated Transponder tag * Tributary_Lookup: factor; the name of the tributary of the Russian River to which the fish was released * Tributary: factor; the name of the tributary to the Russian River where the observation took place * Year: The calendar year of the observation * Date: The date of the observation in format YYYY-mm-dd * Date_Lookup: Date fish was released * Survey: A code specifying the type of survey corresponding to the observation: * ANT: detection on a PIT antenna * DSMT: observations upon capture in a Downstream Smolt Migrant Trap * HAT: observations at the hatchery prior to release * REL: observations during release from hatchery into the river * SEI: observations upon capture during seine surveys * EF: observations upon capture during electrofishing surveys * Site: factor; description of the observation site * SiteCode: factor; abbreviated description of the observation site; RR corresponds to Russian River, WIL corresponds to Willow Creek, numbers correspond to the river kilometer (starting at the downstream-most point) at which the site is located * Species_Lookup: factor; common name of the species corresponding to the observation * ForkLength: the fork length of the fish in millimeters; (blank) indicates it was not measured during that observation * Weight: the weight of the fish in grams; (blank) indicates it was not measured during that observation * PITObsApp: indicates whether the pit tag was observed or applied during that observation for surveys that include handling of fish; (blank) for PIT tag detections on the antenna arrays * HatchYear: the calendar year the fish hatched from its egg; denotes cohort identity * ReleaseSeason: denotes the season the fish was released from the hatchery into the river * "AdultPITNumbers.share.csv": * ReturnWinter: The winter period during which the adult was detected returning from the ocean to spawn * Age: The integer age of the fish, in years, at return * PITNumber: The unique code identifying individual fish that is the tag number from the implanted Passive Integrated Transponder tag. Use as key to join with data in "willow.MS1.csv" * "WIL-antenna-efficiency.csv": * HatchYear: calendar year of hatching (cohort) * SmoltYear: calendar year the fish smolt (HatchYear plus one) * SiteCode: factor; abbreviated description of the observation site; RR corresponds to Russian River, WIL corresponds to Willow Creek, numbers correspond to the river kilometer (starting at the downstream-most point) at which the site is located * p_Oct-Feb: detection efficiency for October to February season * p_Mar-Jun: detection efficiency for March to June season * "dsmt_prop.csv": * HatchYear: calendar year of hatching (cohort) * Hatchery: counts of hatchery fish in the downstream migrant trap * Wild: counts of wild fish in the downstream migrant trap * prop.hatchery: the proportion of DSMT captures that were hatchery fish (i.e. Hatchery/(Hatchery + Wild)) * "releases.csv": * NumberReleased: numeric; the number of fish released from the hatchery * HatchYear: calendar year of hatching (cohort) * "wild.csv": * SiteCode: factor; abbreviated description of the observation site; RR corresponds to Russian River, WIL corresponds to Willow Creek, numbers correspond to the river kilometer (starting at the downstream-most point) at which the site is located * Survey: Survey type; ANT is antenna detection, EF is electrofishing capture * PITNumber: factor; The unique code identifying individual fish that is the tag number from the implanted Passive Integrated Transponder tag * DateTime: datetime of observation; NA except for antenna detections * Date: Date of observation in format yyyy-mm-dd * Lifestage_Lookup: The recorded lifestage at time of tagging (subjective) * Note that "(blank)" denotes information not collected for a given observation and is equivalent to NA ## R Version and Package Versions R version 4.4.0 (2024-04-24) Packages: * betareg 3.2-0 * dataRetrieval 2.7.15 * dplyr 1.1.4 * EflowStats 5.2.0 * forcats 1.0.0 * ggplot2 3.5.1 * knitr 1.46 * lme4 1.1-35.3 * lmerTest 3.1-3 * lubridate 1.9.3 * mclust 6.1.1 * patchwork 1.2.0 * readr 2.1.5 * rstatix 0.7.2 * stringr 1.5.1 * tibble 3.2.1 * tidyr 1.3.1 * tidyverse 2.0.0 * viridis 0.6.5 ## Authors Henry K. Baker (1) Mariska Obedzinski (1,2) Theodore E. Grantham (1) Stephanie M. Carlson (1) 1: Department of Environmental Science, Policy, and Management; University of California, Berkeley 2: California Sea Grant ## Acknowledgments We thank Gregg Horton and colleagues at Sonoma Water for access to these data. We acknowledge the many staff at California Sea Grant and Sonoma Water who contributed to the collection of these data. ## References Horton, G.E., Letcher, B.H. & Kendall, W.L. (2011). A multistate capture–recapture modeling strategy to separate true survival from permanent emigration for a passive integrated transponder tagged population of stream fish. Transactions of the American Fisheries Society, 140, 320–333.