Pacific Salmon & Trout
Phylogeography and diversity
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According to fossil and genetic evidence, the genus Oncorhynchus (Pacific salmon and trout) had diverged by the Miocene (15-20 mya) (Behnke 1991; Devlin 1993). By this era, six species of Pacific salmon had diverged in contrast to only one species of Atlantic salmon (Waples et al. 2008). Pacific salmon speciation was intensified by dynamic geological activity, such as mega floods, volcanic eruptions, and alpine glacial activity, all vastly altering the habitat available to Pacific salmon within the Columbia River Basin during the Miocene (Montgomery 2000). These changes to habitat, affected Pacific salmon populations through population bottlenecks, divergence in isolation, and subsequent range expansion with secondary contact among populations.
Figure 1. Lyle Falls located in the Klickitat River with platforms constructed for fishing.
Life Cycle
Salmonids undertake long migrations (hundreds of KMs) in early life stages and back again to spawn. Spawning occurs in freshwater rivers and streams, emergence of alevins and development into fry continues in freshwater habitats. While migrating, fry experience smoltification, or physiological adaptations, suited to saltwater habitats. Upon ocean arrival, salmonids persist in marine habitats for varied lengths of time, and finally undertake a return migration to spawn. Salmonids exhibit philopatry and return to their natal sites to spawn at relatively predictable times.
Figure 2. Salmonid life cycle.
Migration Timing
Phenotypic traits associated with migration have been demonstrated to be heritable in both juvenile and adult Pacific salmon and trout (Thériault et al., 2007; Carlson & Seamons, 2008). Additionally, migration timing of adult Pacific salmon and trout have also been demonstrated to be heritable (Quinn et al., 2000; Quinn et al., 2015). Further, adult migration timing is associated with a genomic region of major effect in both steelhead and Chinook salmon (O. tshawytscha) (Hess et al., 2016; Prince et al., 2017; Micheletti et al., 2018; Narum et al., 2018; Thompson et al., 2019). Restriction site associated DNA sequencing (RAD-seq) studies have revealed single-nucleotide polymorphisms (SNPs) within the greb1L gene region that are associated with adult migration timing in steelhead (Hess et al., 2016; Prince et al., 2017). Additional whole genome re-sequencing approaches have revealed further SNPs associated with adult migration timing and expanded the genomic region of discovered SNPs to three more candidate genes (rock1, mib1, abhd3, and intergenic region between greb1L and rock1) (Micheletti et al., 2018).
The greb1L gene is broadly present and conserved in vertebrates and the function is believed to be similar to greb1, which has been shown to modulate estrogen receptors and augment the role of estrogen receptor mediated gene expression in humans (Mohammed et al., 2013). Markers shown to have non-conservative and non-synonymous mutations by Micheletti et al. (2018) indicate that this genetic region is under selection and the markers in the intergenic region, upstream of greb1L, associated with adult migration timing could be promoters or enhancers and regulate expression of greb1L (Kilpinen et al., 2013). Recent studies suggest that greb1L plays a role in early and late adult migration phenotypes in steelhead and Chinook salmon (Hess et al., 2016; Prince et al., 2017; Micheletti et al., 2018; Narum et al., 2018; Thompson et al., 2019). Adult migration to spawning grounds is intrinsically linked to sexual development and maturation in Pacific salmon and trout and these processes have been attributed to greb1L in chum salmon (O. keta) and other species (Ghosh et al., 2000; Rae et al., 2006; Pellegrini et al., 2012; Choi et al., 2014).
Figure 3. greb1L and rock1 genes identified as genes with loci associated with migration timing for steelhead with CMH analysis (Micheletti et al. 2018).
Migration Timing
The migration of Oncorhynchus spp. (Pacific salmon and trout) is a critical cultural, economic, and ecological resource throughout their native range. Conservation of salmon and steelhead is based upon maintaining phenotypic and genetic variation of distinct populations and a principal focus involves conserving adult migration timings across large drainages such as the Columbia River basin. Many populations are managed according to degree of reproductive isolation and life history variation. Evolutionarily significant units (ESU) of Pacific salmon and trout are defined as a Distinct Population Segment (DPS) under the US Endangered Species Act (ESA) (Ryder, 1986; Waples, 1991) and each DPS is determined by whether it is sufficiently reproductively isolated and of evolutionary importance to the species (Waples, 1991). Since the late 1800s, wild Pacific salmon and trout have experienced a steady decline in abundance and range. The freshwater range of Pacific salmon and trout has shrunk to about 60% of the historical range (National Research Council, 1996; English et al., 2006). The decline has been initially attributed to overharvest, habitat degradation (logging, mining, agricultural practices), and other anthropogenic development, but modern anthropogenic activity including hydroelectric dams’ disruption of migratory routes, climate change, introgression between native populations and hatchery stocks, and an ongoing decrease in suitable habitat have also contributed to decline (Chapman, 1986; Meehan, 1991; Crozier et al., 2008).
Figure 4. Physical measurements and observations are recorded and genetic samples are collected from non-lethal fin clips at the Lyle Falls adult trap.