Fig 1.
Relationship between adult salmon returns to the San Joaquin basin and the river flows experienced as juveniles.
Fall-run Chinook salmon returns (‘escapement’) to the San Joaquin basin from 1952 to 2011 (CDFW GrandTab, www.CalFish.org) relative to mean flows at Vernalis (USGS gauge 11303500, http://waterdata.usgs.gov/nwis) for the January to June outmigration period they experienced 2.5 years previous. Note that adult abundance estimates have not been corrected for age distributions (we assumed that all adults returned at age 3), inter-annual variation in harvest rates or out-of-basin straying. The large deviation in 2007 reflected poor returns that were attributed to poor ocean conditions [96] and resulted in the closure of the fishery. Adapted from [97].
Fig 2.
The San Joaquin basin of the Central Valley, California (inset).
Map showing the major rivers in the San Joaquin basin, and the location of the rotary screw trap site at Caswell Memorial State Park and USGS gauges at Ripon and Vernalis. The upstream barriers to salmon migration in the three main tributaries are indicated by orange bars.
Table 1.
Adult sample sizes, age structure and collection periods.
Fig 3.
Otolith 87Sr/86Sr reconstructions of a smolt and fry outmigrant.
Otolith 87Sr/86Sr profiles against back-calculated FL for two adult Chinook salmon that returned to the Stanislaus River having outmigrated as (A) a smolt and (B) a fry. The shaded box indicates the time spent rearing in the natal river. The fry outmigrant reared for several weeks downstream in the San Joaquin River before migrating out to the ocean, as indicated by both the left (triangles, solid line) and right (circles, dashed line) otolith (back-calculated FL = 33.3mm vs. 34.9mm). Mean 87Sr/86Sr signatures for the Stanislaus and San Joaquin Rivers, and modern-day ocean are displayed. Black filled symbols indicate ‘re-spots’ carried out to improve sampling resolution. Error bars = 2SE.
Fig 4.
Daily abundance of juvenile salmon outmigrating in 2000 and 2003 relative to ambient environmental conditions.
Juvenile salmon were sampled by rotary screw traps at Caswell as they outmigrated from the Stanislaus, and raw counts were expanded into daily abundance estimates (vertical bars) based on trap efficiency models. River flow (grey line) and maximum daily temperature (orange line) were measured at Ripon (data available at http://cdec.water.ca.gov/). Turbidity (green line) was measured at Caswell [40]. The first instance of temperatures reaching 15°C is indicated by an arrow on each plot.
Table 2.
Abundance and migration timing of juvenile migratory phenotypes.
Fig 5.
Size and phenology of juveniles outmigrants relative to river flow in 2000 and 2003.
Mean (±SD) daily fork length (FL) of juvenile outmigrants, and cumulative percentage of fry (short dashed line), parr (long dashed line) and smolt (solid line) outmigrants relative to flow (filled area). Reference lines indicate the size categories used to define the migratory phenotypes: fry (≤55mm), parr (55-75mm) and smolts (>75mm).
Table 3.
Natal assignments of unmarked adults based on otolith 87Sr/86Sr.
Fig 6.
Size-at-outmigration of the juveniles and surviving adults that left freshwater in 2000 and 2003.
Size-frequency distributions showing the fork length (FL) at which juveniles outmigrated from the Stanislaus River in 2000 and 2003 (grey bars) and the reconstructed size-at-outmigration of the returning (i.e. “successful”) adults from the same cohort (black bars). FLs given in 2mm bins (where the x-axis represents < that value, e.g. "55" = FL 53.01–55.0mm). Size classes used to categorize fry, parr and smolt outmigrants are indicated by dashed lines.
Table 4.
Contribution and survival of fry, parr and smolt outmigrants to the adult escapement.
Fig 7.
Schematic to conceptualize the data sources, methods and results presented in this study.
This figure outlines the life cycle of fall-run Chinook salmon in the California Central Valley. Inset plot (1) demonstrates the abundance of parental spawners in the 1999 and 2002 escapement that contributed to the two focus years. Inset plots (2) and (3) illustrate the abundance and proportions of migratory phenotypes (fry, parr and smolts) observed in the juvenile sample (based on RST sampling) and in the adult escapement (based on otolith reconstructions), respectively. Arrow widths (not to scale) illustrate the typical proportions of 2, 3, 4 and 5 year olds observed in the adult escapement; note that age 5 fish tend to comprise <1% of the returns [50].