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.

1. Reference juvenile otolith and water Sr isotope values [referred to as "Supporting Data S1" in manuscript]

This data file contains reference (“known-origin”) ⁸⁷Sr/⁸⁶Sr 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).

File name: Supporting_Data_S1.csv

2. Priors used to weight natal assignment model

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).

File name: dfa_priors.csv

3. Otolith Sr isotope values for Chinook salmon adults spawning in the Stanislaus River in 2001-2013

This file contains ⁸⁷Sr/⁸⁶Sr 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 ⁸⁷Sr/⁸⁶Sr 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"). 

File name: oto_sr_data_stanislaus_adults_2001-13.csv

4. Summary of natal assignments and – for adults originating in and return to the Stanislaus River – their natal and freshwater exit distances

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).

File name: summary_origin_and_exit_size_by_fish.csv

5. Training data for reconstructing juvenile fork length from otolith radius in California Central Valley fall run juvenile Chinook salmon

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

File name: oto_radius_fork_length_training_data.csv

6. Daily abundance of (a) fry, (b) parr and (c) smolts emigrating from the Stanislaus River in 1996-2014

Daily expanded passage estimates of fry, parr and smolts emigrating from the Stanislaus River in 1996-2014 (fry ≤55mm, parr >55 to <75mm, and smolts >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. 

File names: daily-boot-smolt.csv / daily-boot-smolt.csv / daily-boot-smolt.csv

7. Daily size distribution of juveniles sampled emigrating from the Stanislaus River in 1996-2014

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).

File name: daily_FL_distributions_at_screw_trap.csv

'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.