DOI: 10.5061/dryad.5x69p8dd3
title: Lifetime carryover of early partial migration behaviors in an estuarine-dependent fish under climate change

description: Complex spatial structure within populations confers population stability
 and resilience through asynchronous responses of population sub-components
 to perturbation (i.e., portfolio effect). In fishes, spatial structure
 frequently develops via early-life partial migration, leading to
 diversified nursery use. However, the portfolio effect depends on how
 adult recruitment from different nurseries exhibits asynchronous dynamics
 in response to climate variables, and whether nursery experiences carry
 over to adult demographics. For a three-decade span, we tested adult
 nursery recruitment and carryover effects associated with early-life
 partial migration in Hudson River striped bass. Early-life partial
 migration led to structured utilization of freshwater, brackish, and
 coastal nurseries, all of which recruited to the adult population. Adult
 recruitment from brackish nurseries increased with freshwater flow, while
 coastal nurseries produced more adults during severe winter years.
 First-year nursery experiences carried over to influence adult sex, but
 not growth. Most females utilized brackish nurseries in their first year,
 while adult males recruited from freshwater and brackish nurseries.
 Early-life partial migration led to diversified nursery use and influenced
 adult demographics, which buffered populations against perturbations.
description: # Lifetime carryover of early partial migration behaviors in an
 estuarine-dependent fish under climate change
 [https://doi.org/10.5061/dryad.5x69p8dd3](https://doi.org/10.5061/dryad.5x69p8dd3) This README was generated on 20241219 by K. Arai. Author (Name, Institution, Email): K. Arai, University of California Davis, [kharai@ucdavis.edu](mailto:kharai@ucdavis.edu) This README is in reference to the data sets and R codes (.Rmd) needed to recreate the figures and analyses in “Lifetime carryover of early partial migration behaviors in an estuarine-dependent fish under climate change”, submitted by K. Arai. There are five major analyses within the manuscript. The first script `01_nursery_assignment_2024-07-22.Rmd` reconstructs nursery habitats of adult striped bass using otolith chemistry, time series changepoint analysis, and random forest classification. The second script `02_abundance_environment_2024-07-22.Rmd ` organizes the predictor variables used to model adult brackish and wester Long Island Sound nursery indices. The third script `03_gamlss_2024-07-22.Rmd` runs the Generalized Additive Model for Location, Scale, and Shape (GAMLSS) to investigate the effect of environmental conditions and density-dependence on adult nursery use. The fourth script `04_yoy_adult_comp_2024-07-22.Rmd ` compares the adult brackish nursery index with the young-of-year (YOY) brackish proportion. The fifth script `05_carryover_effects_2024-07-22.Rmd` tests early life carryover effects to adult growth sex characteristics. ## Description of the data and file structure Data list 1. `01_adult_data_2023-02-23.Rds` 2. `01_adult_laicpms_roll_corrected_2023-02-23.Rds` 3. `01_data_edge_2023-02-23.Rds` 4. `02_Annual.indices.of.abundance.csv` 5. `02_Flow_Data_2023-02-21.Rds` 6. `02_Temperature_Data_1921-2021_2023-02-21.Rds` 7. `04_river_section_volume_2023-05-09.csv` 8. `04_Salinity_HRBMP_2023-03-02.Rds` 9. `04_Standing_crop_full.csv` Script list 1. `01_nursery_assignment_2024-07-22.Rmd` 2. `02_abundance_environment_2024-07-22.Rmd` 3. `03_gamlss_2024-07-22.Rmd` 4. `04_yoy_adult_comp_2024-07-22.Rmd` 5. `05_carryover_effects_2024-07-22.Rmd` ### Adult striped bass meta data (`01_adult_data_2023-02-23.Rds`) This data contains collection information of adult striped bass collected in the Hudson River. If the cell involves "NA", this indicates missing or unavailable values due to incomplete data or non-applicable measurements. 1. Number of variables: 15 2. Number of cases/rows: 190 3. Variable list: unique otolith ID (`otolith_id`), unique fish ID (`Fish_ID`), gear type used for collection (`gear`), sampling year (`year`), sampling date (`samp_date`), river kilometer at collection (`rkm`), fish total length in mm (`tl`), fish fork length in mm (`fl`), fish weight in grams (`wt`), fish sex (`sex`), fish maturation stage at collection (`stage`), fish age determined by otoliths in years (`age`), selection for otolith chemistry (`select`), fish year-class (`yearclass`), and other comments associated with the sample (`comments`). ### Adult striped bass otolith chemistry data (`01_adult_laicpms_roll_corrected_2023-02-23.Rds`) This data contains otolith chemistry of adult stiped bass. If the cell involves "NA", this indicates missing or unavailable values due to incomplete data or non-applicable measurements. 1. Number of variables: 21 2. Number of cases/rows: 387967 3. Variable list: unique fish ID (`Fish_ID`), laser ablation scan time (`Time`), distance from the otolith core in µm (`Dist_Core`), 24Mg concentration in ppm (`Mg24_ppm`), 25Mg concentration in ppm (`Mg25_ppm`), 44Ca concentration in ppm (`Ca44_ppm`), 55Mn concentration in ppm (`Mn55_ppm`), 63Cu concentration in ppm (`Cu63_ppm`), 66Zn concentration in ppm (`Zn66_ppm`), 88Sr concentration in ppm (`Sr88_ppm`), 111Cd concentration in ppm (`Cd111_ppm`), 137Ba concentration in ppm (`Ba137_ppm`), 138Ba concentration in ppm (`Ba138_ppm`), 208Pb concentration in ppm (`Pb208_ppm`), unique otolith ID (`otolith_id`), fish sampling year (`year`), fish year-class (`yearclass`), fish age determined by otoliths in years (`age`), fish sex (`sex`), fish total length in mm (`tl`), fish weight in grams (`wt`), ### Young-of-the-year (YOY) striped bass otolith edge chemistry reference data (`01_data_edge_2023-02-23.Rds`) This data contains the otolith chemistry data of young-of-the-year (YOY) stiped bass used as a reference for the random forest classification. If the cell involves "NA", this indicates missing or unavailable values due to incomplete data or non-applicable measurements. 1. Number of variables: 26 2. Number of cases/rows: 3192 3. Variable list: unique fish ID (`Fish_ID`), laser ablation scan time (`Time`), distance from the otolith core in µm (`Dist_Core`), otolith back-calculated fish total length in mm (`TL_bc`), 24Mg concentration in ppm (`Mg24_ppm`), 25Mg concentration in ppm (`Mg25_ppm`), 44Ca concentration in ppm (`Ca44_ppm`), 55Mn concentration in ppm (`Mn55_ppm`), 63Cu concentration in ppm (`Cu63_ppm`), 66Zn concentration in ppm (`Zn66_ppm`), 88Sr concentration in ppm (`Sr88_ppm`), 111Cd concentration in ppm (`Cd111_ppm`), 137Ba concentration in ppm (`Ba137_ppm`), 138Ba concentration in ppm (`Ba138_ppm`), 208Pb concentration in ppm (`Pb208_ppm`), approximate river section at collection (`Subregion`), fish sampling year (`Year`), fish collection date (`Collection_Date`), fish standard length in mm (`SL`), fish total length in mm (`TL`), fish weight in grams (`Weight`), fish age determined by otoliths in days (`Age`), salinity at collection in ppt (`Salinity`), the otolith distance from the core to the start of the otolith edge in µm (`Edge_value`), a categorical variable defining the otolith edge region (`Edge`), salinity zone of the collection site determined by the salinity at collection (`Habitat`). ### Annual indices of abundance for striped bass early life stages (`02_Annual.indices.of.abundance.csv`) This data contains the annual indices of abundance for striped egg, yolk-sac larvae (YSL), post yolk-sac larvae (PYSL), and young-of-year (YOY) obtained from the “Year Class Reports” for the Hudson River Biological Monitoring Program (HRBMP). If the cell involves "NA", this indicates missing or unavailable values due to incomplete data or non-applicable measurements. 1. Number of variables: 4 2. Number of cases/rows: 172 3. Variable list: Year (`Year`), index of abundance (`Index`), standard error (`Std.err`), early life stage type (`Type`). ### Hudson River daily flow data (`02_Flow_Data_2023-02-21.Rds`) This data contains the daily freshwater flow data (1946–2022) obtained from the USGS Green Island monitoring station at the head of HR Estuary. If the cell involves "NA", this indicates missing or unavailable values due to incomplete data or non-applicable measurements. 1. Number of variables: 5 2. Number of cases/rows: 28073 3. Variable list: date of measurement (`Date`), measured flow in cubic meters per second (`flow`), year of measurement (`Year`), month of measurement (`Month`), day of measurement (`Day`). ### Hudson River daily water temperature data (`02_Temperature_Data_1921-2021_2023-02-21.Rds`) This data contains the daily water temperature data (1921–2021) obtained from the Poughkeepsie Water Treatment Facilities and USGS monitoring station below Poughkeepsie. If the cell involves "NA", this indicates missing or unavailable values due to incomplete data or non-applicable measurements. 1. Number of variables: 6 2. Number of cases/rows: 36553 3. Variable list: date of measurement (`Date`), measured water temperature in degrees Celsius (`temp`), the type of station where measurement was made (`Type`), year of measurement (`Year`), month of measurement (`Month`), day of measurement (`Day`). ### Hudson River river section volume data (`04_river_section_volume_2023-05-09.csv`) This data contains the volume of each river section in the Hudson River obtained from the “Year Class Reports” for the Hudson River Biological Monitoring Program (HRBMP). If the cell involves "NA", this indicates missing or unavailable values due to incomplete data or non-applicable measurements. 1. Number of variables: 2 2. Number of cases/rows: 13 3. Variable list: Hudson River river section (`Region`), river section volume (`Volume`). ### Hudson River salinity data (`04_Salinity_HRBMP_2023-03-02.Rds`) This data contains the salinity data of each river section in the Hudson River obtained from the “Year Class Reports” for the Hudson River Biological Monitoring Program (HRBMP). If the cell involves "NA", this indicates missing or unavailable values due to incomplete data or non-applicable measurements. 1. Number of variables: 5 2. Number of cases/rows: 9061 3. Variable list: year of measurement (`Year`), date of measurement (`Date`), Hudson River river section (‘Station’), measured salinity in ppt (`Salinity`), river kilometer of the river section (`RKM`). ### Hudson River striped bass early-life stage standing stocks data (`04_Standing_crop_full.csv`) This data contains the Hudson River striped bass early-life stage standing stocks data obtained from the “Year Class Reports” for the Hudson River Biological Monitoring Program (HRBMP). If the cell involves "NA", this indicates missing or unavailable values due to incomplete data or non-applicable measurements. 1. Number of variables: 17 2. Number of cases/rows: 1483 3. Variable list: collection year (`Year`), collection date (`DATE`), early life stage type (`Type`), standing stock estimates in the Battery (`BT`), Yonkers (`YK`), Tappan Zee (`TZ`), Croton-Haverstraw (`CH`), Indian Point (`IP`), West Point (`WP`), Cornwall (`CW`), Poughkeepsie (`PK`), Hyde Park (`HP`), Kingston (`KG`), Saugerties (`SG`), Catskill (`CS`), Albany (`AL`), and all river sections combined (`COMBINED`). ## Code/Software All analyses were conducted in `R`. The output assumes that the `.Rmd` scripts are placed in a `scripts` folder along with a `data` folder that contains the supplied data, a `figures` folder that is now empty but will contain output figures, and a `outputs` folder that is now empty but will contain outputs of the analyses. Please run the scripts in sequential order from 01 to 05.