DOI: 10.5061/dryad.73n5tb2ss
title: Unnatural selection of salmon life histories in a modified riverscape

description: Altered river flows and fragmented habitats often simplify riverine
 communities and favor non‐native fishes, but their influence on
 life‐history expression and survival is less clear. Here, we quantify the
 expression and ultimate success of diverse salmon emigration behaviors in
 an anthropogenically altered California river system. We analyzed two
 decades of Chinook salmon monitoring data to explore the influence of
 regulated flows on juvenile emigration phenology, abundance, and
 recruitment. We then followed seven cohorts into adulthood using otolith
 (ear stone) chemical archives to identify patterns in time‐ and
 size‐selective mortality along the migratory corridor. Suppressed winter
 flow cues were associated with delayed emigration timing, particularly in
 warm, dry years, which was also when selection against late migrants was
 the most extreme. Lower, less variable flows were also associated with
 reduced juvenile and adult production, highlighting the importance of
 streamflow for cohort success in these southernmost populations. While
 most juveniles emigrated from the natal stream as fry or smolts, the
 survivors were dominated by the rare few that left at intermediate sizes
 and times, coinciding with managed flows released before extreme summer
 temperatures. The consistent selection against early (small) and late
 (large) migrants counters prevailing ecological theory that predicts
 different traits to be favored under varying environmental conditions.
 Yet, even with this weakened portfolio, maintaining a broad distribution
 in migration traits still increased adult production and reduced variance.
 In years exhibiting large fry pulses, even marginal increases in their
 survival would have significantly boosted recruitment. However, management
 actions favoring any single phenotype could have negative evolutionary and
 demographic consequences, potentially reducing adaptability and population
 stability. To recover fish populations and support viable fisheries in a
 warming and increasingly unpredictable climate, coordinating flow and
 habitat management within and among watersheds will be critical to balance
 trait optimization versus diversification.
description: <b>1. Reference
 juvenile otolith and water Sr isotope values [referred to as
 "Supporting Data S1" in manuscript]</b> This data file contains reference
 (“known-origin”) <sup>87</sup>Sr/<sup>86</sup>Sr
 values measured in otoliths from juvenile Chinook salmon collected from
 rotary screw traps within their natal stream and water samples collected
 throughout the Central Valley, plus their source. The juvenile
 otolith samples were used to train a discriminant function analysis to
 classify adult salmon to their hatchery or river of origin (adult otolith
 dataset described below). The water data were used to understand isotopic
 variation along their migration pathway from the Stanislaus River to the
 ocean and to interpret both natal and freshwater exit in the otoliths of
 returning adults (Fig. 1 of main manuscript). <i>File
 name: Supporting_Data_S1.csv</i> <b>2. Priors used to weight
 natal assignment model</b> We applied these priors to our
 discriminant function analysis to classify adults to a river or hatchery
 of origin using strontium isotope values measured in the natal region of
 the otolith. These priors were based on straying rates into the Stanislaus
 River based on coded wire tag recoveries in the Constant Fractional
 Marking Program (detailed in Supporting Information). Note that natal
 assignments to the Stanislaus River (“returns”) changed very little
 whether we used a weighted or unweighted DFA (increasing confidence in the
 resulting stray rates used to estimate recruitment - see Supporting
 Information). <i>File name:
 dfa_priors.csv</i> <b>3. Otolith Sr isotope
 values for Chinook salmon adults spawning in the Stanislaus River in
 2001-2013</b> This file contains
 <sup>87</sup>Sr/<sup>86</sup>Sr values measured in
 otoliths from adult Chinook salmon sampled from the spawning grounds
 of the Stanislaus River, California, between 2001 and 2013. Fish age was
 estimated using scale annuli to match individuals to our focus emigration
 cohorts: 1999, 2000, 2003, 2004, 2008, 2009, 2011. Each otolith contains
 multiple <sup>87</sup>Sr/<sup>86</sup>Sr values,
 representing spot analyses sampled along a standardized 90° transect from
 the otolith core towards the otolith edge (ending once the individual had
 entered the ocean). We included a subset of coded wire tagged (CWT) adults
 to test the accuracy of our classification model – these were excluded
 from subsequent analyses. If no CWT code provided the fish was
 unmarked and of unknown origin. The average isotopic value of the natal
 region (tagged “y” here) was used to assign the fish to a river or
 hatchery of origin (see above for training samples). Strays were excluded
 from further analysis, but for individuals that had originated in and
 returned to the Stanislaus River, we estimated natal and freshwater exit
 based on when their profile deviated from the natal range and exceeded our
 freshwater threshold value (described in the paper and Supporting
 Information). This data file also includes the uncertainty around each
 spot measurement based on instrument error ("2SE") and the
 strontium voltage ("SrV").  <i>File name:
 oto_sr_data_stanislaus_adults_2001-13.csv</i> <b>4. Summary of natal
 assignments and – for adults originating in and return to the Stanislaus
 River – their natal and freshwater exit distances</b>
 Here we include the river
 or hatchery of origin assigned to each unmarked adult spawner based on
 their otolith strontium isotope profiles. Site codes are described in the
 priors files, above. For returns to the Stanislaus River (site code = STA)
 we also estimated natal and freshwater exit size (‘OR’ = otolith radius;
 FL = reconstructed fork length, see Fig. S2 and training data
 below). <i>File name:
 summary_origin_and_exit_size_by_fish.csv</i> <b>5. Training data for
 reconstructing juvenile fork length from otolith radius in California
 Central Valley fall run juvenile Chinook salmon</b> This file contains paired otolith
 radius and fork length (FL) measurements for 294 juvenile fall run Chinook
 salmon from the California Central Valley. We used a segmented model (Fig.
 S2 of Supporting Information) to reconstruct FL at natal and freshwater
 exit in returning adults to the Stanislaus River. We also provide a walk
 through of the code used to build the model at https://github.com/annasturrock/Oto_size_fish_size_calibration <i>File name: oto_radius_fork_length_training_data.csv</i> <b>6. Daily abundance of (a) fry, (b) parr and (c) smolts emigrating from the Stanislaus River in 1996-2014</b> Daily expanded passage estimates of fry, parr and smolts emigrating from the Stanislaus River in 1996-2014 (fry ≤55mm, parr &gt;55 to &lt;75mm, and smolts &gt;75mm), based on rotary screw trap captures at Caswell State Park near the confluence with the San Joaquin River. More details on the expansion methods provided in Sturrock et al. (2015) PLoS ONE 10(5): e0122380 and in Zeug et al. (2014) Fisheries Management and Ecology, 21(2), 155-168. Note that dangerous flows in 1997 and 2006 precluded sampling for extended periods during those years, so we excluded these years from subsequent analysis in the paper. Note that the total annual abundances (and their associated confidence intervals) and emigration timings by phenotype are provided in the Supporting Information.  <i>File names: daily-boot-smolt.csv / daily-boot-smolt.csv / daily-boot-smolt.csv</i> <b>7. Daily size distribution of juveniles sampled emigrating from the Stanislaus River in 1996-2014</b> This file provides fork length frequencies for a random subset of juveniles caught in the screw trap each day. These size distributions were applied to the daily expanded passage estimates (above) to create the size distribution of natal exit sizes expressed by the emigrating juveniles each year (Fig. 6a of main paper). <i>File name: daily_FL_distributions_at_screw_trap.csv</i>
description: 'ASN' numbers represent the agency ID given to each
 fish. Further details are provided in the paper and its Supporting
 Information. Please do not hesitate to contact the corresponding author
 (asturrock@ucdavis.edu) if you have any questions or queries.