General Information

1. Author Information A. Corresponding Author Name: Stephanie Carlson Institution: University of California, Berkeley Email: smcarlson@berkeley.edu B. Co-investigator Contact Information Name: Eric Huber Institution: University of California, Berkeley Email: eric.r.huber@gmail.com C. Co-investigator Contact Information Name: Rachael Ryan Institution: University of California, Berkeley Email: rachael_ryan@berkeley.edu D. Co-investigator Contact Information Name: Rachel Johnson Institutions: NOAA Fisheries, Southwest Fisheries Science Center & University of California, Davis Email: rachel.johnson@noaa.govD. Co-investigator Contact Information E. Name: Anna Sturrock Institution: University of Essex Email: anna.sturrock@essex.ac.uk F. Co-investigator Contact Information Name: Robert Lusardi Institution: University of California, Davis Email: ralusardi@ucdavis.edu <br>
2. Dates that data spans: 1948-2017 (hatchery release data)
3. Geographic locations where data was collected: Coleman National Fish Hatchery (located on Battle Creek, California); Nimbus Fish Hatchery (located on the American River, California); Feather River Fish Hatchery (located on the Feather River, California); Mokelumne River Fish Hatchery (located on the Mokelumne River, California)
4. Species data is collected on: Central Valley Steelhead trout (Oncorhynchus mykiss), a Distinct Population Segment listed as threatened under the Endangered Species Act
5. Data sources: The data presented was not collected by the authors but sourced from annual reports, electronic databases, and compiled reports from California Department of Fish and Wildlife, U.S. Fish and Wildlife Service, California Hatchery Scientific Review Group, Regional Mark Information System.

Abstract

The California Central Valley steelhead (Oncorhynchus mykiss) has declined precipitously since Euro-American colonization and has been listed as threatened under the United States Endangered Species Act since 1998. Hatchery-origin fish now dominate the population and hatchery management is a key listing factor. However, scant release metric information is available. We compiled a time series of O. mykiss hatchery release data for all four Central Valley hatcheries releasing O. mykiss between 1948 and 2017. The biocomplexity of released fish has declined since the early 1980s. Individuals have been released at increasingly similar numbers, biomass, body sizes, times, and locations over time. Moreover, yearling fish have been released at larger sizes, leading to the near-exclusive release of age-1 smolts in February and March since the late 1990s and early 2000s. Pervasive reductions in release portfolios have likely occurred for other hatchery-supported Pacific salmonid stocks throughout the Pacific Rim region. In an increasingly variable environment, such reductions in intraspecific diversity could significantly affect population stability and resilience.

Keywords: Artificial propagation, biocomplexity, growth, life history, Oncorhynchus mykiss, phenotypic
diversity, portfolio effect, stocking

Data Description

This dataset has two main components, organized into folders:

• RELEASE_DATA
  • CV_Steelhead_Hatchery_Release_Database.csv
• OBJECTIVES_FIGURES
  • Manuscript Figures Script
    • CV_Omykiss-FINAL-MS-Figs.html
  • Objective 1: Temporal trends in juvenile releases
    • CVSH_totmill.csv
    • CVSH_biom.csv
    • CVSH_RelTot_revised.csv
    • CVSH_violin_hatchdist.csv
    • CVSH_mass_at_release_violin_data.csv
    • CVSH_age_at_rel_violin_data.csv
    • CVSH_fig8_lifehist.csv
    • CVSH_propyrling.csv
  • Objective 2: Temporal variation in juvenile release metrics
    • CVSH_DI.csv
    • CVSH_CV_all_update_May2021.csv
  • Supplement 1
    • FigS1_data.csv
  • Supplement 2
    • FigS2.1_data_AGR.csv
    • FigS2.1_age_mass.csv

RELEASE_DATA Compiled datasets of all hatchery release data, in a csv file, compiled from a variety of sources and put into a workable database. Useful for future analyses that require information on hatchery release practices (date of release, size at release, number released).

OBJECTIVES_FIGURES Contains an RMarkdown document converted to HTML that outlines the code used to create figures in the associated manuscript, and all data files (11 .csv files) with calculated metrics used for figures to achieve objectives laid out in the manuscript. Data files are organized by objective (1-3). Figures created using this code include Figures 2-8, S1.1, S1.2, S1.4, S1.5, S1.6, S1.7, S1.8, S2.1 (all found in Huber et al. 2024, CJFAS).

Refer to the README files within each component folder for a further description and breakdown of the data.

Methods

Release Database Compilation

We compiled release data from 135 annual reports provided by the California Department of Fish and Wildlife (CDFW) for state-operated hatcheries. The state hatchery annual reports spanned one fiscal year from 1 July to 30 June of the following year: NFH (54 reports, 1956–57 to 2009–10), FRFH (40 reports, 1969–70 to 2009–10), and MRFH (41 reports, 1964–65 to 2007–08). From 1988 to 2001 release records were obtained for MRFH from the California Hatchery Scientific Review Group (CA HSRG 2012, Appendix VI) instead of annual reports because the former dataset is more detailed and complete. From 2001-2017 for the FRFH and 2003- 2017 for the NFH and MRFH, an electronic dataset from CDFW's statewide inventory system was used instead of annual reports or California Hatchery Scientific Review Group data (CA HSRG 2012, Appendix VIII). Hatchery release data were considered “draft” or non-finalized from 1994-2017 for the NFH, 1992-2017 for the FRFH, and 1988-2017 for the MRFH. Release data for the CNFH from 1948 to winter 1975 were obtained from an electronic database provided by the U.S. Fish and Wildlife Service (USFWS) and data from spring 1975 to 2017 were obtained from the Regional Mark Information System (RMIS, http://www.rmpc.org/, retrieved on 21 May 2020).

The basic reporting unit for all data sources was a cohort of similarly sized fish released together in a stated release location over a specified time (hereafter referred to as a “release group”). Information about brood year (same as emergence year for winter-run O. mykiss), total number of fish planted, average or range of fish size(s)-at-release (usually expressed as fish·lb-1), release timing (from single days to months), and descriptions and (or) geographic coordinates of release locations were reported for release groups. Total numbers of returning O. mykiss trapped at state hatcheries were compiled from annual reports and the electronic database provided by CDFW.

Resulting databases: CV_Steelhead_Hatchery_Release_Database.csv

Objective 1: Temporal trends in juvenile releases

Number released We present annual release data according to the California ‘water year’ (WY; 1 October to 30 September) since this period is more relevant to the Central Valley O. mykiss life cycle than calendar years (e.g., upstream migration in fall and winter, spawning and emergence in winter, rearing in spring and summer [Williams 2006]). When the release period spanned two WYs (5.1% of total number released, 90.5% of which occurred before WY 1976), the WY possessing the larger share of the release period was assigned as the release WY. In rare instances when the release period spanned two WYs and was split equally between WYt and WYt+1 (0.2% of all releases), WYt+1 was set as the release year. A three year moving average was applied to the annual numerical release data to highlight longer-term trends.Data file used: CVSH_totmill.csv

Biomass released Release group biomass was calculated as the product of total number of fish released and mean fish mass for that release group. The mean annual fish mass-at-release for a hatchery was used as the mean mass-at-release for any release group’s missing weight, length, or life history stage-at-release information (3.8% of all releases). A three year moving average was also applied to the annual biomass release data to smooth the time series data.Data file used: CVSH_biom.csv

Release timing We analyzed release timing at the monthly scale because release day of month was missing for 63.5% of all releases. The release period usually occurred within the same calendar month (80.3% of all releases) but occasionally a range of calendar months were reported (16.7% of all releases). In limited cases, only release year was reported (3.0% of all releases). Due to these inconsistencies, we restrict all release timing and growth rate analyses to cases when the release start and end months were the same.Data file used: CVSH_RelTot_revised.csv

Release location Geographic coordinates of release locations and river km distances from the releasing hatchery to the release location were obtained from Sturrock et al. (2019) (92.0% of all releases), RMIS (1.4% of all releases), or the electronic database provided by CDFW (0.7% of all releases). An additional 5.7% of release location coordinates and hatchery distances were newly determined using the methods described by Sturrock et al. (2019). Coordinates and distances are not available for 0.2% of all released fish due to insufficient descriptions of release site locations.
Data file used: CVSH_violin_hatchdist.csv

Size-at-release Fish sizes were reported as mean mass (75.2% of all releases) or length (19.5% of total) for each release group. To facilitate dataset comparisons, length-at-release was converted to mass-at-release (and vice versa) according to the following relationship for Sacramento River O. mykiss (Hallock et al. 1961):

ln(M) = ln (8.80 ∙ 10 ―6) + 3.06 ∙ ln(FL)

Where mass is in measured grams and fork length is measured in millimeters. Note that this (M) (FL) relationship was determined for fish with FLs equal to or larger than 325 mm but predicts masses for smaller fish within 5% deviation from a similar length-weight transformation reported for California Central Coast O. mykiss (Huber 2018; 53-442 mm FL range; R2=0.99) across nearly the entire O. mykiss size range encountered in this investigation (97.0% of all hatchery fish with reported lengths smaller than 325 mm FL were larger than 53 mm FL). When size ranges were reported, the midpoint was assigned as the mean length or mass for the release group. Occasionally missing size data could be gleaned from written descriptions of the release group’s life history stage (e.g., “fry”, “fingerlings”, “yearlings”). In these cases (1.5% of all releases), the midpoint of the life stage-at-release mass range (see “Life-stage-at-release” below) was used.
Data file used: CVSH_mass_at_release_violin_data.csv

Age-at-release All age information was estimated based on an assumed 1 February spawn date (Satterthwaite et al. 2010) and, therefore, should be considered apparent ages. Age analyses were restricted to cases when the release group beginning and end months of release are identical (80.3% of all releases). Apparent ages were estimated as the difference between release month midpoint and 1 February of the brood year.
Data file used: CVSH_age_at_rel_violin_data.csv

Life-stage-at-release We explored both coarse and fine scale trends in the composition of life- stages-at-release. We first classified O. mykiss as sub-yearling (y-) or yearling or older fish (y+). We followed hatchery program guidelines (CA HSRG 2012, Appendix VIII) and assumed O. mykiss became yearlings once they grew to 71.2 g (~180 mm FL). We further classified life history stage-at-release diversity according to fish sizes and standardized nomenclature guidelines (IEP Steelhead PWT 1998). “Yolk-sac fry” were defined as fish with masses <0.3 g; “fry”: ≥0.3 to 1.4 g; “parr”: ≥1.4 g to <26.3 g; “silvery parr”: ≥26.3 g to <71.2 g; “small smolts”: ≥71.2 g to <131.6 g; “large smolts”: 131.6 g to <219.6g; “subadults”: ≥219.6 g to <954.0 g; and “adults”: ≥954.0 g. For cases when size data were missing but life-stage-at-release was described, “fed fry” were assumed to be fry, “fingerlings” were assumed to be parr, “advanced fingerlings” were assumed to be silvery parr, and “smolts” were assumed to be small smolts.
Data files used: CVSH_fig8_lifehist.csv and CVSH_propyrling.csv

Objective 2: Temporal variation in juvenile release metrics

Life stage diversity We characterized life stage diversity by calculating the Reciprocal Simpson’s Index (RSI; Simpson 1949) for each hatchery and all hatcheries combined per release year. The RSI measures the evenness of a community and ranges from 0 (all life stages were equally represented in every release group) to 1 (all fish were planted at the same life stage).
Data file used: CVSH_DI.csv

Interannual variation in release metrics To investigate interannual variation in release practices, we divided the 70-year time series (1948-2017) into seven 10-year intervals and calculated the decadal coefficient of variation (CV) for six metrics associated with hatchery releases summarized CV10 annually at each hatchery and for all O. mykiss hatchery programs combined. The metrics examined included (1) total number released, (2) total biomass released, (3) mean release month, (4) mean release distance downstream of hatchery, (5) mean mass-at-release, and (6) mean age-at-release: CV10 = SD10/x, where x is the 10-year or decadal mean of the release metric annual totals or means for each hatchery or all hatcheries combined and is the decadal standard deviation for each hatchery or all SD10 O. mykiss programs combined.
Data file used: CVSH_CV_all_update_May2021.csv

Statistical analyses

Prior to data analysis, we removed all release groups from the final database that were known to be for research purposes (usually numbering in the 10s or 100s of fish), out-of-basin releases, and (or) releases in landlocked waters because these fish were not part of the California Central Valley O. mykiss population (0.3% of all releases). All annual and overall mean values presented for release metrics were weighted according to the total number of fish released across all release groups for each hatchery or all O. mykiss hatchery programs combined. Temporal trends of release metrics were quantified using a combination of post-hoc (1) calculations of means of annual means and CVs (standard deviation divided by mean), (2) regression analyses, including linear (ordinary least squares), quadratic, and logistic curve fitting, and (3) residual analyses of linear regressions. To explore evidence of a trend through time, we tested whether the slopes from linear regression analyses differed from zero (i.e., when p<0.05). Statistical analyses were performed using the statistical software R (R Core Development Team 2020) and PAST (version 4.03; Hammer et al. 2001).
For some of the analysis performed: CV_Omykiss-FINAL-MS-Figs.html

Supplement 1

Refer to methods for "Interannual variation in release metrics". Similar methods were applied for each hatchery individually.
Data file used: FigS1_data.csv

Supplement 2

In Supplement 2, we present information about apparent somatic growth rates and sizes-at-age for individual hatcheries and all hatcheries combined.
Data file used: FigS2.1_data_AGR.csv, FigS2.1_age_mass.csv