DOI: 10.5061/dryad.vhhmgqp1p
title: Reproductive success of hatchery- and natural-spawning sockeye salmon, Auke Creek, Alaska

description: Evaluating salmon hatchery supplementation programs requires assessing not
 only program objectives but identifying potential risks to wild
 populations as well. Such evaluations can be hampered by difficulty in
 distinguishing between hatchery- and wild-born returning adults. Here, we
 conducted three years (2011–2013) of experimental hatchery supplementation
 of sockeye salmon in Auke Lake, Juneau, Alaska where a permanent weir
 allows sampling and genotyping of every returning adult (2008–2019). We
 identified both hatchery- and wild-born returning adults with parentage
 assignment, quantified the productivity (adult offspring/spawner) of
 hatchery spawners relative to that of wild spawners, and compared run
 timing, age, and size at age between hatchery- and wild-born adults.
 Hatchery-spawning females produced approximately six to 50 times more
 returning adults than did naturally spawning females. Supplementation had
 no discernable effect on run timing and limited consequences for size at
 age, but we observed a distinct shift to younger age at maturity in the
 hatchery-born individuals in all three brood years. The shift appeared to
 be driven by hatchery-born fish being more likely to emigrate after one,
 rather than two, years in the lake but the cause is unknown. In cases when
 spawning or incubation habitat is limiting sockeye salmon production,
 hatchery supplementation can be effective for enhancing the number of
 returning adult fish but not without the risk of phenotypic change in the
 recipient population, which can be an undesired outcome of hatchery
 supplementation. This study adds to a growing body of evidence suggesting
 that phenotypic change within a single generation of captive spawning
 might be widespread in salmon hatchery programs.
description: From 2008 to 2019, each returning adult sockeye salmon that
 ascended to Auke Lake was captured at the Auke Creek weir, on the outlet
 of Auke Lake, and identified based on the appearance of the snout and vent
 as a female, regular-sized male, or “jack” (precocious male ≤ 400 mm
 mid-eye to fork length) male.  Each salmon had an axillary process removed
 and stored in 95% ethanol for subsequent DNA extraction and genotyping.
 Fish were sampled every day during the run, and all were sampled for
 genotypes. A sub-sample (~12% of the total run) was sampled each year for
 age (from scales) and length (mid-eye to fork) data. Sampling was intended
 to be representative across the entire run. Over three
 successive years (2011–2013), sockeye salmon were artificially spawned and
 their progeny were reared to the early fry stage prior to release into
 Auke Lake. A small number of adults (&lt;50 per year, averaging 2.5%
 of the total run annually) were captured at the weir, retained for
 broodstock, held at the hatchery in tanks (≈ 6 weeks) until mature, and
 subsequently spawned. The target for broodstock was 30 females and 15
 males with a 2:1 breeding design (each male crossed with two females).
 Fertilized eggs were placed in vertical flow incubators fed by water from
 a 2.3 m deep intake in Auke Lake. Emergent fry were ponded and given
 starter feed (Pacific Bio-Products, Inc.) at the manufacturer’s size- and
 temperature-dependent recommendations for optimal growth; this
 captive-rearing period lasted for ≈ 4 weeks. Each year, ≈ 50,000 fry (≈
 0.3 g) were released into several locations in the limnetic zone of Auke
 Lake, where they were allowed to feed and grow alongside wild-born
 individuals and emigrate volitionally to the ocean after one or two years
 in freshwater. Sockeye salmon return to Auke Creek 3–6 years after birth
 (Kovach et al. 2014), so returning adults that were born in captivity
 would return over the years 2014–2019. Genotyping was
 conducted at the Gene Conservation Lab of the Alaska Department of Fish
 and Game. Genomic DNA was extracted using DNeasy® 96 Tissue Kit (Qiagen).
 Samples were genotyped at 9 short tandem repeat (STR) and 45 single
 nucleotide polymorphism (SNP) markers. Taqman assays and the Fluidigm
 Biomark 96.96 and 48.48 Dynamic Arrays were used to genotype the SNPs,
 following the methods outlined in Seeb et al. (2009). Amplification of STR
 loci was carried out in 10 µL reaction volumes and PCR fragments were
 identified on an Applied Biosystems 3730 capillary DNA sequencer. PCR
 bands were visualized and separated into bin sets using AB GeneMapper
 software v4.0 and automated binning was subsequently confirmed or
 corrected manually. A subsample (8 of every 95 individuals) was
 re-extracted and genotyped to quantify genotyping error rate.
 Seeb, J. E., Pascal, C. E., Ramakrishnan, R. Seeb, L. W. (2009).
 SNP genotyping by the 5′-nuclease reaction: Advances in high-throughput
 genotyping with nonmodel organisms. In: A. Komar (Ed.), Methods in
 Molecular Biology: Single-nucleotide Polymorphisms, 2nd edition (pp.
 277-292). New York: Humana Press.
description: # Reproductive success of hatchery- and natural-spawning sockeye salmon,
 Auke Creek, Alaska This
 dataset consists of phenotypic (sex and adult return migration timing for
 all sampled fish; length and age for a subsample) and genotypic data on
 all adult sockeye salmon returning to Auke Lake, Juneau, Alaska, from 2008
 to 2019. Genetic data were used to assign adult offpsring to parents, and
 from those assignments calculate relative productivity, or the average
 number of returning adult offspring produced by hatchery spawners relative
 to that of wild spawners over three brood years (2011-2013). These data
 were also used to determine if phenotypes of hatchery-born fish differed
 from those born in the wild. Hatchery spawning was successful, with
 captive spawners producing between 6 to ~50 x the number of returning
 offspring than wild spawners. Hatchery-born fish did not differ from
 wild-born fish in return timing or size at age, but they tended to be
 younger on average.  ## Description of the data and file structure The
 data are in two .csv files. The first, "SAUKE_Genotypes_V13.csv"
 consists of genotypic data for each individual fish at 9 microsatellite
 (or short tandem repeat) and 45 single nucleotide polymorphism (SNP) loci.
 Fish have two individual identifiers: 1) "SillyCodeID", which is
 used by the Alaska Department of Fish and Game Gene Conservation Lab for
 tracking samples: and 2) "franzID" which is a 10-character
 individual ID for use in the parentage program FRANz. The franzID takes
 the format yytsnnnnnn, where yy is the two-digit year of return (e.g., 08
 for 2008), t is the type as spawning adult (h = hatchery, w = wild) and s
 is the "sex" identified at the weir (f = female, m = male, j =
 "jack" or precocial male). n represents the numeric fish ID,
 which matches the number of the SillyCodeID. The genotypes are in the
 format "allele1/allele2". An allele identified as "-"
 represents a scored null allele. A "?" in a allele position
 represents missing data (i.e., no allele call). The second data file,
 "SAUKE_DemographicInformation_V12.csv" contains additional
 information about each fish sampled. The first 2 columns are the
 individual fish identifiers and are identical to those described for the
 genotypes file. The remaining columns are: * ReturnYear - year of sampling
 at the weir * DateCollected: day sampled at the weir * Sex: f = female, m
 = male, j = "jack" (precocial male) * TypeAsSpawningAdult:
 hatchery = spawned in the hatchery; hatchery_not_spawned = selected for
 broodstock but never spawned; mortality = died at the weir; radiotagged =
 radiotagged for a different study; wild = spawned in the wild *
 MidEyeForkLength = length (mm) from middle of the eye to the fork of the
 caudal fin * ScaleAge: age as determined from scales, where the first
 digit represents number of annuli in freshwater, second is number of
 annuli in saltwater. e.g., 1.1 is 1 year in freshwater, 1 in salt, and is
 a three-year old fish (first winter is in the gravel as egg/embryo and not
 recorded on scale). Entries with characters rather than integers, e.g.,
 "i.i" ,"r.2", "x.x", represent unreadable
 scales; entries with question marks, e.g., "2.2?" indicates the
 reader is not confident in the scale age. * AgeYearsScales = total age
 calculated from a scale; e.g., a fish with a 2.2 scale age spent 1 winter
 incubating prior to scale formation; 2 winters in freshwater, and 2
 winters in saltwater so is 5 years old * Comments: any additional comments
 made during sample collection or preparation. For more information contact
 the author. In "SAUKE_Genotypes_V13.csv" the value
 "NA" indicates missing data (e.g., most fish were not sampled
 for length or scales). The two datasets can be linked to each other via
 franzID. ## Sharing/Access information None. ## Code/Software Data were
 analyzed in R. Scripts for data analysis are available at