Microsatellite allelic and mitochondrial DNA (mtDNA) haplotype diversity are analyzed in eight rainbow trout (Oncorhynchus mykiss) collections: two from tributaries flowing into the upper Santa Ynez River watershed at Gibraltar Reservoir (Camuesa and Gidney creeks); three from tributaries between Gibraltar and Jameson reservoirs (Fox, Blue Canyon, and Alder creeks); one from a tributary above Jameson Reservoir (Juncal Creek); Jameson Reservoir; and one from the mainstem Santa Ynez River above the Jameson Reservoir. Both analyses reveal a high degree of population structure. Thirteen microsatellite loci are amplified from 376 fish. Population pairwise comparisons show significant differences in allelic frequency among all populations with the exception of Juncal Creek and Jameson Reservoir (p = 0.4). Pairwise F_st values range from 0.001 (Juncal Creek and Jameson Reservoir) to 0.17 (Camuesa and Juncal creeks) with an overall value of 0.021. Regression analyses (Slatkin 1993) supports an isolation-bydistance model in the five populations below Jameson Reservoir (intercept = 1.187, slope = -0.41, r2 = 0.67). A neighbor-joining bootstrap value of 100% (based on 2000 replicate trees) separates the populations sampled above and below Juncal Dam.

Composite haplotypes from 321 fish generated using mtDNA sequence data (Dloop) reveal four previously described haplotypes (MYS1, MYS3, MYS5 and MYS8; Nielsen et al. 1994a), and one (MYS5) was found in all populations. Mean haplotype diversity is 0.48. Pairwise F_st values from mtDNA range from -0.019 to 0.530 (0.177 over all populations) and are larger than those for microsatellites in 26 of 28 pairwise comparisons. In addition, the mtDNA and microsatellites provide contrasting evidence of the relationship of Fox and Alder creeks to the other six populations. Discrepancies between the two markers are likely due to the unique properties of the two marker types and their value in revealing historic (mtDNA) versus contemporary (microsatellites) genetic relationships. The contrasting results may indicate how relationships among the upper Santa Ynez River populations have changed since the installation of Juncal Dam.

Comparisons of mtDNA haplotype frequencies from fish collected for this study with samples analyzed previously in JLN’s laboratory (1993) reveal significant differences in mtDNA haplotypes for Fox and Alder creeks. In the 2001 samples from this study, there is a loss of three haplotypes despite larger sample sizes. AMOVA analysis of what we term “upper” (Alder, Fox, Blue Canyon, Camuesa, Gidney creeks and the upper Santa Ynez mainstem) and “lower” (Hilton, Salsipuedes and the lower mainstem Santa Ynez River) Santa Ynez River populations (1993-2001) reveal that 11% of the variance in haplotypes is found between the upper and lower drainage. A comparison of the mtDNA data from this study with those available for southern California coastal and California hatchery O. mykiss populations yields F_st values of 0.15 and 0.47, respectively. Differentiation of mtDNA haplotypes for population pairs of Santa Ynez River and hatchery fish show no significant differentiation between wild and at least one hatchery strain in Cachuma Reservoir, Hilton Creek, and the Lower Santa Ynez River.