DOI: 10.5061/dryad.bzkh189n3
title: Photoperiod at emergence regulates early life history plasticity in fall Chinook salmon

description: Early life history pathways for Chinook salmon are directly related to
 environmental variation, which can shift phenotypic traits expressed by a
 population. Fall Chinook salmon in the upper Columbia River Basin
 historically timed migration downstream (smolted) as subyearlings, however
 some wild and hatchery reared fall Chinook salmon also express a
 successful yearling smolt life history strategy. Previous research
 suggests that this shift to yearling smoltification represents evolution –
 a genetic change due to an increase in fitness and improved downstream
 survival. Alternatively, the shift in smolt timing could be a
 phenotypically plastic response that optimizes life history traits for
 current environmental conditions. We raised hatchery-origin fall Chinook
 salmon from the Umatilla River (Oregon, USA) in a controlled laboratory
 experiment to explore environmental drivers of early life history. We
 found smolt timing to be age/size dependent for subyearlings, and
 photoperiod dependent for yearlings. We found the propensity for
 precocious male maturation at age-1 (microjack) to be primarily
 photoperiod dependent and for age-2 (minijack) to be primarily growth
 dependent. The resulting adaptable life history portfolio may provide this
 population with some baseline capacity to cope with future environmental
 change.
description: # Photoperiod at emergence regulates early life history plasticity in fall
 Chinook salmon
 [https://doi.org/10.5061/dryad.bzkh189n3](https://doi.org/10.5061/dryad.bzkh189n3) ## Description of the data and file structure We raised hatchery origin fall Chinook salmon from the Umatilla River (Oregon, USA) in a controlled laboratory experiment designed to describe and define phenotypic plasticity for age of smoltification and early male maturation. At the time of ponding, fry were exposed to one of three photoperiod treatments: Winter Solstice (WS), Early Spring (ES), and Late Spring (LS). For each photoperiod treatment, there were two replicated feed treatments (high and low feed) resulting in a total of 6 unique treatments (12 total tanks of fish).  Throughout the investigation, fish were monitored for growth, smoltification (via seawater challenges and gill Na+/K+-ATPase activity), and age and prevalence of early (“precocious”) male maturation. ### Files and variables #### File: UMA\_FCS\_BY11\_Minijack\_data\_Final.csv **Description:** This file contains raw data for individual males identified at the termination of the experiment for each photoperiod treatment ##### Variables * Date: Calendar date of measurement * Tank Number: Treatment system tank number (1-12) * Treatment: feed/emergence treatment abbreviations: 'WSHF' = Winter Solstice high feed ; 'WSLF' = Winter Solstice low feed ; 'ESHF' = Early Spring high feed ; 'ESLF' = Early Spring low feed; 'LSHF' = Late Spring high feed ; 'LSLF' = Late Spring low feed * Fish Number: Individual fish sample number/ID * FL_mm: Fork lengths measured to the nearest mm. * WT_g: Weight of fish measured to the nearest g. * NOTE: Comments on physical appearance of abnormal fish * Sex_Visual: sex and maturation status of males based on visual assessment of gonadal development. 'M' = immature male; 'MD' = maturing age-2 male; 'MD/MP' = male that matured age 1 and age 2; 'MD?' = possible age 2 mature male; 'UM' = unknown status (missing 11KT value) * 11KT_ng/ml: 11-ketotestosterone levels, ng/ml (n/a for none available because of lab error or not enough plasma collected) * Sex_11KT: sex and maturation status of males based on 11-ketotestosterone levels; 'M' = immature male; 'MD' = maturing age-2 male; 'MD/MP' = male that matured age 1 and age 2; assay thresholds varied by experimental tank as described in methods. Missing data code: N/A #### File: UMA\_FCS\_BY11\_SeawaterChallengeData\_Final.csv **Description:** This file contains raw data from fish included in the 72-hr seawater challenges over the course of the experiment  ##### Variables * Photo_trt: emergence treatment abbreviations: 'WS' = Winter Solstice; 'ES' = Early Spring; 'LS' = Late Spring * Feed_trt: feed treatment abbreviations: 'H' = High Feed; 'L' = Low Feed * Iso_tank: Treatment system tank number * SW_tank: Seawater challenge system tank number * Surv_time: Survival time (in days from beginning of challenge, day 4 survivors were sacrificed) * status: 2 = mortality, 1=survived challenge * sample_period: Seawater challenge number (1-16) * age_DPP: Age of fish in days post ponding * FL: Fork Length of fish to nearest mm * W: Weight of fish to nearest g * Sex: U=undetermined, M=male, F=Female #### File: UMA\_FCS\_BY11\_ATPase\_Final.csv **Description:** This file contains raw data from fish sacrificed for physiological sample collection (gill tissue) to analyze Na+/K+-ATPase activity ##### Variables * Sample Date: Calendar date of sample collection * Assay Date: Calendar date ATPase assay was conducted * Tank#: Treatment system tank number * Treatment group: feed/emergence treatment abbreviations: 'WSHF' = Winter Solstice high feed ; 'WSLF' = Winter Solstice low feed ; 'ESHF' = Early Spring high feed ; 'ESLF' = Early Spring low feed; 'LSHF' = Late Spring high feed ; 'LSLF' = Late Spring low feed * Fish: Individual fish number/sample ID * ATPase: ATPase activity value determined by assay (μmol PO4∙mg protein-1∙h-1) * Length: fish fork length in mm * Weight: fish weight in g * Sex: sex and maturation status of fish based on visual assessment of gonadal development. 'U'=undetermined;'F' = Female; 'M' = immature male; 'MD' = maturing age-2 male; 'MD?' = possible age 2 mature male #### File: UMA_FCS_BY11_BatchWeights_Final.csv **Description:** This file contains raw data for batch weights conducted throughout the experiment to monitor fish weight for adjustment of rations and to track growth ##### Variables * Date: Calendar date of weight measurement * Tank: Treatment system tank number * Treatment: feed/emergence treatment abbreviations: 'WSHF' = Winter Solstice high feed ; 'WSLF' = Winter Solstice low feed ; 'ESHF' = Early Spring high feed ; 'ESLF' = Early Spring low feed; 'LSHF' = Late Spring high feed ; 'LSLF' = Late Spring low feed * \#fish/batch: Number of fish per batch weight measurement * Weight B1: Batch one weight in grams * Weight B2: Batch two weight in grams * Weight B3: Batch three weight in grams #### File: UMA_FCS_BY11_MicrojackData_Final.csv **Description:** This file contains raw data collected on the number of males identified as precocious parr (age-1) throughout the experiment ##### Variables * Treatment: feed/emergence treatment abbreviations: 'WSHF' = Winter Solstice high feed ; 'WSLF' = Winter Solstice low feed ; 'ESHF' = Early Spring high feed ; 'ESLF' = Early Spring low feed; 'LSHF' = Late Spring high feed ; 'LSLF' = Late Spring low feed * Tank_number: Treatment system tank number * PP_take down: Precocious parr identified at termination of experiment * Males_take down: Number of males identified at termination of experiment * PP_fall screen: Precocious parr identified at November 2012 screen * Males_fall screen: Number of males identified at November 2012 screen * PP_morts: Precocious parr identified as mortalities during entire experiment * PP_total: Total number of precocious parr * Males_total: Total number of males * PP_proportion: Proportion of precocious parr out of all males ## Code/software All fish growth/size data and maturation logistic regression models were analzyed with STATA 15.1 (StataCorp LLC) Fish gill Na+K+-ATPase activity was analyzed using R version 4.1.2 Seawater challenge survival was analyzed using non-parametric Kaplan Meier Survival Curves, as well as a Cox Proportional Hazards (CPH) Model using R version 4.1.2 and the packages “survival” and “survminer”. The survival heatmap (figure 4) was generated using R version 4.1.2, and the ggplot2 package