Little is known of the genetic basis of migration despite the ecological benefits migratory species provide to their communities and their rapid global decline due to anthropogenic disturbances in recent years. Using next generation sequencing of restriction-site associated DNA (RAD) tags we genotyped thousands of SNPs in two wild populations of migratory steelhead and resident rainbow trout (Oncorhynchus mykiss) from the Pacific Northwest of the United States. One population maintains a connection to the sea, whereas the other population has been sequestered from its access to the ocean for more than fifty years by a hydropower dam. Here we performed a genome-wide association study (GWAS) to identify 504 RAD SNP markers from several genetic regions that were associated with the propensity to migrate both within and between the populations. Our results corroborate those in previous quantitative trait loci (QTL) studies and provide evidence for additional loci associated with this complex migratory life history. Our results suggest a complex multi-genic basis with several loci of small effect distributed throughout the genome contributing to migration in this species. We also determined that despite being sequestered for decades, the landlocked population continues to harbor genetic variation associated with a migratory life history and ATPase activity. Furthermore we demonstrate the utility of genotyping-by-sequencing and how RAD-tag SNP data can be readily compared between studies to investigate migration within this species.

Homing and straying in salmon have been extensively studied, yet it has proven difficult to disentangle the biotic and abiotic factors that influence straying. In the Columbia River basin, some juvenile salmon are collected at dams and transported downstream to increase survival during seaward migration, and as returning adults they experience a range of environmental conditions as they ascend the river. We examined 8 years of PIT tag detection data for hatchery-reared, fall-run Chinook Salmon Oncorhynchus tshawytscha released in the Snake River to evaluate the combined effects of juvenile barging, rearing and release locations, and environmental conditions on adult migration speed and straying below and above the Columbia River-Snake River confluence. Straying to the upper Columbia River was 10-19 times more likely among adults that were barged as juveniles from Snake River dams than among adults that were in-river migrants or that were transported from McNary Dam (below the confluence) as juveniles. Similarly, barging from Snake River dams and warmer Columbia River temperatures increased the likelihood of straying into streams below the confluence. Furthermore, adult upstream migration was slower among

This study evaluated whether a population of adfluvial redband trout Oncorhynchus mykiss gairdnerii (a subspecies of rainbow trout) in Mann Creek and Reservoir, southwestern Idaho, continues to undergo smoltification. This population had an anadromous component before the construction of main-stem and tributary dams in 1958 and 1967, respectively. Smoltification was assessed by quantifying the proportion of juvenile migrants that displayed high skin reflectance, comparing mean gill Na + ,K + -ATPase activity among migrants, and examining migration timing compared with that of neighboring steelhead (anadromous rainbow trout) populations. Approximately one-quarter of the 1,502 juvenile migrants trapped and examined displayed the intermediate or high skin reflectance (nonbanded silvery coloration) characteristic of smolts; the other fish maintained a banded coloration more typical of resident fish. For 78 samples of gill filaments over the course of the migration season (18 March to 3 June), Na + ,K + -ATPase activity varied considerably among fish (0.95-5.81 µmol Pi · h −1 · mg protein −1 ) and doubled in nonbanded fish over the course of the migration period. ATPase activity was significantly higher for nonbanded fish than for banded fish at the end of the migration period (21 May -4 June). Juvenile adfluvial redband trout migrated from Mann Creek in approximate synchrony with neighboring steelhead populations. These results suggest the possibility that in areas in the Snake River drainage where steelhead have been extirpated as a result of artificial barriers, remnant populations retain the potential for anadromy.

We measured summer microhabitat use, availability, and selection by age-0 Chinook salmon Oncorhynchus tshawytscha in the Big Creek drainage, Idaho. Age-0 fish selected for low-velocity (0-25 cm/ s), moderate-depth (40-80 cm) habitats that were located within 80 cm of cover. Pools (52%) and runs (38.5%) were the most commonly used habitat types, while pebbles (33.7%) and sand (23%) were the most often used substrates. Cover type use was predominated by woody debris (54.8%) and rock outcrops (23.7%). Run (38.5%) and riffle (32.9%) were the most available habitats in Big Creek, while pebble (38.4%) and cobble (28.2%) were the most available substrates. Mean water velocity (47 cm/s) availability and distance to cover (108 cm) availability were greater than those selected by age-0 Chinook salmon, while mean total water depth (30 cm) availability was lower than that selected by the fish. Linear regression was used to show that an increase in juvenile Chinook salmon total length was significantly (P , 0.05) related to increased total water depth (r 2 ¼ 0.68), focal water depth (r 2 ¼ 0.73), and focal water velocity (r 2 ¼ 0.49) use. The relationship of habitat use and fish total lengths indicate that even within a short temporal period, juvenile Chinook salmon will select for different habitats as they grow. Upper and lower Big Creek microhabitat availability characteristics differed significantly (P , 0.05). Upper Big Creek had more fish per unit of preferred rearing habitat than lower Big Creek, which suggests that either summer microhabitat availability or redd density partially explain the density differences observed in Big Creek. Microhabitat use and availability data were useful for identifying habitat selection of age-0 Chinook salmon in Big Creek. The data from this study can be used for future identification, quantification, and restoration of suitable Chinook salmon rearing habitat in other Pacific Northwest streams.

In this study we collected information on abundance, age structure, migration, and exploitation to characterize the population demographics and reproductive characteristics of a historically anadromous Columbia River Redband Trout Oncorhynchus mykiss gairdneri population now isolated in a southwestern Idaho reservoir and limited to resident and adfluvial life histories. We estimated there were 3,905 adfluvial individuals in Mann Creek Reservoir in October 2008 based on a mark-recapture population estimate. The adfluvial population sex ratio of 2.78 females per male captured at a weir, peak spawn timing near the peak of the hydrograph (late April), age at spawning (4-6 years), and growth patterns (slow growth in the stream followed by rapid growth in the reservoir) were all characteristic of an anadromous population. Resident fish abundance was not estimated, but the fish were characterized by relatively slow growth, earlier sexual maturity, and a reverse sex ratio (0.23 females per male) compared with the adfluvial fish. The two life histories (resident and adfluvial) and their differential use by the sexes are consistent with life history theory, which suggests female salmonids maximize fitness by increasing body size and fecundity while males attempt to maximize survival at the expense of growth. The migratory fish in this drainage that could have historically exercised an anadromous life history appear to be exercising the next-best option, an adfluvial life history, which has relatively similar costs and benefits to the anadromous form as distinct from the stream-resident form. Future studies should evaluate other similar native populations isolated in reservoir systems because these populations could play a role in recovery of endangered steelhead (anadromous Rainbow Trout) populations in the western USA.