California Golden Trout (Oncorhynchus mykiss aguabonita)

For more information contact Molly Stephens:

Background and Significance of Study

California golden trout Oncorhynchus mykiss aguabonita were used extensively in the first half of the 20th century to stock lakes and streams throughout the western United States (Pister 1991). The source of these stocks have been attributed to an introduction of fish from either Golden Trout Creek (a tributary of the Kern River) or the South Fork Kern River (Stanley Stephens, California Department of Fish and Game, pers. comm..) to fishless Mulkey Creek (a tributary of the South Fork Kern River) prior to 1876. Twelve fish from Mulkey Creek were subsequently transplanted into Cottonwood Creek (1876) and from there into the Cottonwood Lakes (1891), which served as the source populations for stocks planted throughout the Sierra Nevada, including headwater Lakes draining into the Golden Trout Creek watershed (i.e. Johnson, Chicken Springs, and the Rocky Basin Lakes).

Recent evidence based on protein allozyme analyses have indicated that the Cottonwood Creek and Cottonwood Lakes populations of California golden trout may have become introgressed with alleles from introduced rainbow trout O. m. mykiss, and that introgressed fish may have been subsequently transplanted into Johnson, Chicken Springs, and the Rocky Basin Lakes (Leary 1997). This was confirmed by a recent study (Cordes et al. 2006) of the Golden Trout Creek drainage, which confirmed low and localized areas of introgression at the site of these introductions. A more recent study evaluated South Fork Kern River populations of California golden trout and found a strikingly different pattern of introgresssion (Figure 1), with high levels of rainbow trout influence present in the lower reaches and tributaries of the South Fork Kern, corresponding to rainbow trout stocking in the lower reaches of this river (Cordes et al. 2003).

California golden trout map image

Figure 1. Comparison of admixture levels detected in Golden Trout Creek and South Fork Kern River California golden trout populations.


Materials and Methods

Sample Collections: Fin clips samples of California golden trout were collected by California Department of Fish and Game personnel throughout the Golden Trout Creek and South Fork Kern River drainages. Rainbow trout samples were taken from hatchery and wild populations to use as references.

Data Collection and Analysis:

  • Six microsatellite loci
  • One single copy nuclear minisatellite
  • 18 SNP loci
  • Admixture analysis using ADMIX and STRUCTURE


Microsatellite loci were used to assess population structure and introgression in California golden trout in Golden Trout Creek (Cordes et al. 2006) and the South Fork Kern River (Cordes et al. 2003; manuscript in review). Recently developed SNP markers were used in a comparative study of microsatellite versus SNP marker estimates of introgression (Stephens et al., in prep). This study has confirmed the ability of SNP markers to assess introgression in California golden trout populations in the South Fork Kern (Figure 2).

California golden trout data analysis graph image

Figure 2. STRUCTURE representation of SNP data analysis for South Fork Kern California golden trout.
Each vertical bar represents an individual fish, with populations grouped by population number (as in Table 1) on the x-axis. The green bar color indicates “rainbow trout” group membership, while red denotes “golen” group membership. The presence of green, therefore, indicates rainbow trout admixture in a given individual at levels measured by proportion on the y-axis.

Future Work

We are currently applying SNP markers to assessment of introgression in the Golden Trout Creek watershed. A manuscript of comparison between SNP and microsatellite admixture estimates in California golden trout is in preparation (Stephens et al., in prep)



This work is progressing in collaboration with the California Department of Fish and Game (CDFG).

Funding is provided by the CDFG and the US Fish and Wildlife Service.