SNP Discovery for Upper McCloud redband trout (Oncorhynchus mykiss stonei)


Background and Significance

The McCloud River Redband Trout (MRRT), Oncorhynchus mykiss stonei, is a threatened form of coastal rainbow trout (Oncorhynchus mykiss sp.; RBT) native to the Upper McCloud River, a tributary to the Sacramento River. MRRT populations are threatened by a number of factors, including small population size, introgression, and drought.

During the drought of 2015-2016, California Department of Fish and Wildlife (CDFW) conducted a fish rescue to remove fish from one of the four known pure populations of MRRT, Sheepheaven Creek, which was drying out. The rescued fish were used to found a conservation hatchery which will release brood stock into local waters for both conservation of MRRT and the promotion of a recreational fishery. While potentially a beneficial conservation strategy, stocking from a hatchery that cultures both RBT and MRRT introduces risk of introgression that requires genetic monitoring.

This project is using RAD sequencing data to develop genetic tools (SNP markers) to monitor native, reintroduced, and stocked MRRT populations. We have identified SNP markers designed for high throughput genetic analyses of introgression between pure MRRT and RBT and for monitoring overall population genetic diversity. These markers will allow managers to identify and adapt to changing patterns of introgression and genetic diversity, and to make informed decision for conservation prioritization.

Methods and Preliminary Results

To date we have completed analyses of structure and admixture on a number of native and introgressed trout populations from throughout the state (Figure 1; Table 1). Below are some PCA and admixture plots that depict population structure and grouping within and among our samples (Figures 2 and 3). 

Figure 1. A map of the northern populations sample for this project, including redband trout and MRRT. Additional locations were sampled but are outside the range of this map.



Table 1. Source of the redband and MRRT samples that were used, along with sample year and watershed. Locations are depicted in the map above (Figure 1). Additional samples were included but are not listed on this table.



Figure 2. An admixture plot with K=5 that includes all of our samples. Dark blue is California golden trout, light blue is Little Kern golden trout and Kern River rainbow trout, yellow = hatchery RBT, eagle lake RBT, and steelhead,  green = redband trout, and orange = MRRT.



Figure 3. A PCA plot created with NGSAdmix depicting the populations from the Upper McCloud basin. This plot shows some structuring, with the pure populations of Swamp, Edson, Sheepheaven, and Dry each showing some substructure.


Project Status

We have submitted potential SNP markers to CDFW and are currently working on building a phylogenetic tree with known groups of native CA O. mykiss ssp. Our groups include California Golden trout, Little Kern golden trout, Kern River rainbow trout, Warner Valley redband trout, Eagle Lake rainbow trout, Upper McCloud River rainbow trout, and Goose Lake trout. We will be speaking at AFS Reno in October and submitting a manuscript for publication before 2020. 

More information

Simmons, R. E., P. Lavretsky, and B. May. Introgressive Hybridization of Redband Trout in the Upper McCloud River Watershed. Trans. Am. Fish. Soc. 139:201-213 (pdf).


This project is funded with a State Wildlife Grant through California Department of Fish and Wildlife - Agreement #P1781006