Above photos from left to right: Oncorhynchus gilberti, aguabonita, stonei, and irideus

Trout subspecies relationships

Various attempts have been made to elucidate the systematic relationships among native inland trout subspecies through a variety of techniques, from morphological to molecular.  Anthropogenic influences over the past 150 years have also superimposed a signature of introgression between native and introduced rainbow trout.  Of particular conservation concern are the golden and redband trout, many of which have been reduced to small portions of their native ranges.  Establishing clear systematic relationships of remaining “pure” populations of these native trout is critical to their conservation.  It is also critical for establishing the appropriate reference populations for use in developing new genetic markers for these subspecies.  We undertook a multispecies genetic analysis of several trout subspecies native to California using Amplified Fragment Length Polymorphism (AFLP) markers.  The genome-wide survey that AFLP gives allows us to better examine the overall differentiation among these major groups using a highly polymorphic, neutral, nuclear marker.

This research has found Sheepheaven redband, a form of Sacramento redband trout, to be highly distinct from all other redband groups, including Northern Great Basin, Columbia Basin, Warner Basin and even other Sacramento redbands (Figure 1).  Reference populations were established for other native trout subspecies.  

SNP marker development

We recently developed Single Nucleotide Polymorphism (SNP) markers for the detection of rainbow trout introgression in several native trout subspecies (Sprowles et al. in press; table 1). Populations evaluated in this marker development included: Volcano Creek (California golden trout), Upper Soda Springs Creek (Little Kern golden trout), Sheepheaven Creek (McCloud redband trout), Davis Creek (Sacramento redband trout), North Fork American River (wild rainbow trout) and Mount Shasta strain (hatchery rainbow trout).   SNPs were detected in all subspecies and are currently being utilized to detect rainbow trout introgression in native California golden trout,  Little Kern golden trout, and redband trout and also redband trout population genetic relatedness.  We are also currently developing SNP markers for use in studies of introgression between native Paiute cutthroat and introduced rainbow trout.