Research

Freshwater rearing capacity of the Columbia River Basin

Currently, I am using long-term smolt trap and redd counts data from throughout the Columbia River Basin in concert with a stream channel model developed by Tim Beechie and Hiroo Imaki at NOAA to assess the productive capacity of freshwater habitats to produce salmon. We empirically estimate capacity by fitting stock-recruit models to the available data. At the same time, we combine digitized stream reaches (estimates of available habitat) with a channel form model to estimate how much habitat was historically available on the landscape, and assign fish densities (derived form stream surveys) to each channel type. This “habitat expansion” approach allows us to estimate capacity under different scenarios of habitat amount and access on broad spatial scales.

Chinook straying from natal waters while ascending the Columbia River

My post-doctoral research with collaborators: Tom Quinn (UW), Peter Westley (UAF) and Andy Dittman (NOAA) involved evaluating rates of straying by Chinook and steelhead in the Columbia River basin. The Columbia R. provides a unique opportunity to look at straying (i.e. fish that do not return to spawn in their natal stream) because large numbers of fish are tagged, and an extensive array of antennas is actively searching for tags. We used existing datasets of passive integrated transponder (PIT) tagged fish to track where fish went when they came back to the Columbia River as adults. As operators of transport barges, the US Army Corps of Engineers (US ACE) is interested in whether barging juvenile fish through dams, to keep them from going through the turbines, results in higher rates of straying when they come back as adults. With a large PIT tag database, we compared fish from different sources (hatchery, wild) and migration routes (run of the river, transported) to look at what the effects of each was on straying.

Ecology and behavior of Dolly Varden

In my doctoral work in the University of Washington School of Aquatic and Fishery Sciences, I employed Dolly Varden in SW Alaska as a model organism to understand the consequences of residency and anadromy in a system where both strategies appear in sympatry. I used several methods for investigating what strategies the fish are taking, and for evaluating the consequences of those strategies:

Tagging and tracking

In the Chignik Lakes watershed, I tagged Dolly Varden in marine waters with sonic transmitting tags to monitor their movement into freshwater habitats, evaluate the timing of anadromous migrations, and coarsely, what overwintering habitats are being used. In the Chignik system, we are able to couple these movements with counts at a weir operated by the Alaska Department of Fish and Game near the upper reaches of tidal influence.

Otolith microchemistry

Beginning in 2008, I collected Dolly Varden in habitats throughout the Chignik Lakes watershed in summer months to identify the age of each individual, prior migration history, and whether their mother was anadromous in the season of spawning. To perform these analyses I removed otoliths (earbones) from each fish. Otoliths serve as a permanent record of the water chemistry that the fish has encountered throughout its life. By sectioning the otoliths and removing a small trough of material from the core (natal portion) to the edge (recent portion) and analyzing it with a mass spectrometer, we can learn how many times the fish has been to sea, at what age it began ocean migrations, as well as whether there is a strong ocean signature in the core; indicating whether the mother acquired egg resources immediately prior to spawning.

Relative growth rates

In collaboration with the environmental physiology group at NOAA’s NWFSC, I investigated the use of insulin-like growth factor-1 (IGF-1) concentrations in blood, as a proxy for somatic growth in Dolly Varden. This is particularly useful in a large stream-lake network where mark and recapture studies are not feasible, and will allow us to identify the relative changes in growth among various rearing habitats in the Chignik system (e.g. Lagoon, Lake, River)

Foraging ecology

Several studies of Dolly Varden diets exist, although almost all relate to the consumption of salmon fry or smolts. These studies were conducted to determine the efficacy of Dolly Varden bounties that existed in Alaska from the 1920’s through the 40’s. However, most studies indicated that Dolly Varden do not consume many salmon fry or smolts. Instead, researchers often found that in spring and early summer Dollies appeared to have empty, atrophied stomachs. In addition, those fish that did consume prey often appeared to be specializing in particular prey items. My study includes observation of Dolly Varden diets throughout the summer months in concert with stable isotope analysis to determine whether specialization does occur, and whether it is related to specfic life-histories.

Population structure

In collaboration with Penny Crane at the USFWS in Anchorage, I am identifying the level of genetic population structure that exists in the Chignik Lakes watershed, using neutral microsatellite loci. In particular we aim to determine:

  1. whether there is any evidence of spawning segregation within anadromous portions of the watershed
  2. How population structure is associated with hydrologic features within the watershed
  3. In the future this analysis may serve as a baseline to determine rearing habitats for resident and anadromous individuals.

Central California Steelhead ecology

Steelhead and lagoons

In Scott Creek, a central California stream, I conducted my master’s work at UC Santa Cruz with researchers at NOAA’s SWFSC. In 2002 we established a (now) long term research project focusing on steelhead and coho salmon habitat use, growth, survival and hatchery-wild interactions. Scott Creek is of particular interest because it is essentially the southernmost stream with coho salmon in their native range. In addition it is the site of some of the famous study of steelhead and coho life histories by Leo Shapovalov and Alan Taft.

Steelhead in Scott Creek make extensive use of a small estuary that regularly closes during low flow periods from mid-summer until early winter. Early in our studies we determined that juvenile steelhead were experiencing rapid growth in the lagoon habitat. The signature of this rapid growth is left in wide circuli spacing on the scales, forming a permanent record of lagoon residence. After several years at sea, steelhead return to Scott Creek, and some are captured at the weir operated by NOAA. Non-lethal scale sampling indicated that the vast majority of returning steelhead bore the marks of lagoon residence, despite a relatively small portion of the overall population using that habitat. In later years, we validated the scale results with passive integrated transponder (PIT) tags. PIT tags also proved useful in determining the fate of many tagged salmon smolts whose tags ended up on nearby Ano Nuevo island. For more information about the Scott Creek lagoon studies see: Hayes et al. 2008, and Bond et al. 2008