R. Bruce MacFarlane

Marine survival of steelhead (Oncorhynchus mykiss) enhanced by a seasonally closed estuary

To investigate the role that estuaries play in the survival of steelhead, Oncorhynchus mykiss, we compared juve- nile size at ocean entry with back-calculated measures of size at ocean entry for returning adults in Scott Creek, a repre- sentative California coastal stream. During the annual spring emigration, the largest smolts (>150 mm fork length (FL)) move directly to sea, while some smaller smolts remain in the estuary until sandbar formation creates a closed freshwater lagoon. High growth rates in the estuary throughout the summer result in a near doubling of fork length from the time of estuary entry (mean FL of spring migrants = 102.2 mm; mean FL of fall lagoon resident = 195.9 mm). Analysis of the scale morphology of returning adult steelhead indicates that there is strong size-dependent mortality at sea, with estuary- reared steelhead showing a large survival advantage, comprising between 87% and 95.5% (based on tag returns and scale analysis, respectively) of the returning adult population despite being between 8% and 48% of the annual downstream mi- grating population. Although the estuary forms less than 5% of the watershed area, it is critical nursery habitat, and steel- head population persistence in southern margin ecosystems may well depend upon healthy estuaries.

Over the Falls? Rapid Evolution of Ecotypic Differentiation in Steelhead/Rainbow Trout (Oncorhynchus mykiss)

Adaptation to novel habitats and phenotypic plasticity can be counteracting forces in evolution, but both are key characteristics of the life history of steelhead/rainbow trout (Oncorhynchus mykiss). Anadromous steelhead reproduce in freshwater river systems and small coastal streams but grow and mature in the ocean. Resident rainbow trout, either sympatric with steelhead or isolated above barrier dams or waterfalls, represent an alternative life-history form that lives entirely in freshwater. We analyzed population genetic data from 1486 anadromous and resident O. mykiss from a small stream in coastal California with multiple barrier waterfalls. Based on data from 18 highly variable microsatellite loci (He = 0.68), we conclude that the resident population above one barrier, Big Creek Falls, is the result of a recent anthropogenic introduction from the anadromous population of O. mykiss below the falls. Furthermore, fish from this above-barrier population occasionally descend over the falls and have established a genetically differentiated below-barrier subpopulation at the base of the falls, which appears to remain reproductively isolated from their now-sympatric anadromous ancestors. These results support a hypothesis of rapid evolution of a purely resident life history in the above-barrier population in response to strong selection against downstream movement.

Steelhead Growth in a Small Central California Watershed: Upstream and Estuarine Rearing Patterns

We monitored growth and life history pathways of juvenile steelhead Oncorhynchus mykiss and compared growth rates between the upper watershed and estuary in Scott Creek, a typical California coastal stream. Growth in the upper watershed was approximately linear from May to December for age-0 fish. For passive integrated transponder (PIT) tagged, age-1þ fish, growth transitioned to a cyclic pattern, peaking at 0.2% per day during February-April, when maximum flows and temperatures of 7-128C occurred. Growth of PIT-tagged fish then slowed during August-September (0.01% per day), when temperatures were 14-188C and flows were low. During each spring, smolts (mean fork length (FL) 6 SE ¼ 98.0 6 1.2 mm) and fry migrated to the estuary; some fish remained there during summer-fall as low flows and waves resulted in seasonal sandbar formation, which created a warm lagoon and restricted access to the ocean. Growth in the estuary-lagoon was much higher (0.2-0.8% per day at 15-248C). Our data suggest the existence of three juvenile life history pathways: upper-watershed rearing, estuary-lagoon rearing, and combined upper- watershed and estuary-lagoon rearing. We present a model based upon the above data that reports size at age for each juvenile life history type. The majority of fish reaching typical steelhead ocean entry sizes (;150- 250 mm FL; age 0.8-3.0) were estuary-lagoon reared, which indicates a disproportionate contribution of this habitat type to survival of Scott Creek steelhead. In contrast, steelhead from higher latitudes rear in tributaries during summer, taking several years to attain ocean entry size.

Energy dynamics and growth of Chinook salmon (Oncorhynchus tshawytscha) from the Central Valley of California during the estuarine phase and first ocean year.

The greatest rates of energy accumulation and growth in subyearling Chinook salmon (Oncorhynchus tshawytscha) occurred during the first month following ocean entry, supporting the importance of this critical period. Data from an 11-year study in the coastal ocean off California and the San Francisco Estuary revealed that juvenile salmon gained 3.2 kJ·day–1 and 0.8 g·day–1, representing 4.3%·day–1 and 5.2% day–1, respectively, relative to estuary exit values. Little gain in energy (0.28 kJ·day–1) or size (0.07 g·day–1) occurred in the estuary, indicating that the nursery function typically ascribed to estuaries can be deferred to initial ocean residence. Calculated northern anchovies (Engraulis mordax) equivalents to meet energy gains were one anchovy per day in the estuary (8% body weight·day–1) and about three per day immediately following ocean entry (15% body weight·day–1). Energy content in the estuary was positively related to higher salinity and lower freshwater outflow, whereas in the ocean, cooler...

A New Low-Cost Instream Antenna System for Tracking Passive Integrated Transponder (PIT)-Tagged Fish in Small Streams

Abstract We present a new, low-cost, low-power, half/full-duplex passive integrated transponder (PIT) tag interrogation antenna for use in detecting fish movements in small streams. New technology by Allflex-USA allowed us to develop a reading system with an antenna 279.4 cm wide × 60.9 cm high that reads both common tag types used in fisheries today for about US

Diel movements of out-migrating Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) smolts in the Sacramento/San Joaquin watershed

1,000. An instream antenna of this size and price makes high-resolution tracking of fish movement in small streams feasible where cost and tag-type restrictions were prohibitive. For evaluation, we placed the antenna upstream of a small estuary on the central California coast to observe the diel movements of juvenile steelhead Oncorhynchus mykiss between the estuary and upstream habitats in both spring and fall months.

Managed Metapopulations: Do Salmon Hatchery 'Sources' Lead to In-River 'Sinks' in Conservation?

We used ultrasonic telemetry to describe the movement patterns of late-fall run Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (O. mykiss) smolts during their entire emigration down California’s Sacramento River, through the San Francisco Bay Estuary and into the Pacific Ocean. Yearling hatchery smolts were tagged via intracoelomic surgical implantation with coded ultrasonic tags. They were then released at four upriver locations in the Sacramento River during the winters of 2007 through 2010. Late-fall run Chinook salmon smolts exhibited a nocturnal pattern of migration after release in the upper river. This is likely because individuals remain within a confined area during the day, while they become active at night and migrate downstream. The ratio between night and day detections of Chinook salmon smolts decreased with distance traveled downriver. There was a significant preference for nocturnal migration in every reach of the river except the Estuary. In contrast, steelhead smolts, which reside upriver longer following release, exhibited a less pronounced diel pattern during their entire migration. In the middle river, Delta, and Estuary, steelhead exhibited a significant preference for daytime travel. In the ocean Chinook salmon preferred to travel at night, yet steelhead were detected on the monitors equally during the night and day. These data show that closely related Oncorhynchus species, with the same ontogenetic pattern of out-migrating as yearlings, vary in migration tactic.

Striped bass populations in Chesapeake and San Francisco Bays: Two environmentally impacted estuaries

Maintaining viable populations of salmon in the wild is a primary goal for many conservation and recovery programs. The frequency and extent of connectivity among natal sources defines the demographic and genetic boundaries of a population. Yet, the role that immigration of hatchery-produced adults may play in altering population dynamics and fitness of natural populations remains largely unquantified. Quantifying, whether natural populations are self-sustaining, functions as sources (population growth rate in the absence of dispersal, λ>1), or as sinks (λ<1) can be obscured by an inability to identify immigrants. In this study we use a new isotopic approach to demonstrate that a natural spawning population of Chinook salmon, (Oncorhynchus tshawytscha) considered relatively healthy, represents a sink population when the contribution of hatchery immigrants is taken into consideration. We retrieved sulfur isotopes (34S/32S, referred to as δ34S) in adult Chinook salmon otoliths (ear bones) that were deposited during their early life history as juveniles to determine whether individuals were produced in hatcheries or naturally in rivers. Our results show that only 10.3% (CI = 5.5 to 18.1%) of adults spawning in the river had otolith δ34S values less than 8.5‰, which is characteristic of naturally produced salmon. When considering the total return to the watershed (total fish in river and hatchery), we estimate that 90.7 to 99.3% (CI) of returning adults were produced in a hatchery (best estimate = 95.9%). When population growth rate of the natural population was modeled to account for the contribution of previously unidentified hatchery immigrants, we found that hatchery-produced fish caused the false appearance of positive population growth. These findings highlight the potential dangers in ignoring source-sink dynamics in recovering natural populations, and question the extent to which declines in natural salmon populations are undetected by monitoring programs.

A summary of the use of electronic tagging to provide insights into salmon migration and survival

Abstract Striped bass populations have declined precipitously in both Chesapeake Bay and the San Francisco Bay Delta system. Parallel declines in both systems indicate possible common climatic patterns or trends affecting both populations. Climatic instability on both coasts with accompanying changes in average rainfall, outflow and temperature may be interacting with deteriorating water quality and pollution resulting in declining populations of striped bass in both areas. Declines in east coast striped bass stocks have been attributed to: overfishing; nutrient enrichment of the habitat and the resultant, temperature-oxygen squeeze on subadults; deterioration of the near-shore habitat for juvenile striped bass resulting from the loss of submerged aquatic vegetation; decreased survival of larval striped bass due to environmental pollution; poor nutritional state of larvae; and fluctuations in the physical environment and predation. In the San Francisco Bay Delta area the decline has been attributed to the interactive effects of reduced freshwater outflow and increased freshwater diversion, and decreased bay flushing and increased pollutant burdens which have adversely affected both egg production and egg and larval survival.

An introduction to the use of electronic tagging to provide insights into salmon migration and survival

IntroductionThe status of Pacific salmon populations has been ofincreasing concern for many decades, with many pop-ulations now under legal protection. The causes oftheir declining status are manifold and untanglingthem has been difficult due to the complex life histo-ries, which involve migrations among freshwater, es-tuarine, and marine habitats. Finding solutions tosalmon management problems requires understandinghow salmon respond to threats in these different envi-ronments. Telemetry provides an attractive approachto monitoring salmon as they move among these envi-ronments, and advances in miniaturization and massproduction have made it feasible to monitor salmonthroughout their life cycle.Recent advances in acoustic telemetry have provid-ed for the first time an opportunity to greatly expandknowledge and understanding of mortality and themigratory behavior of salmonids on the western coastof North America. Firstly, these electronic tags havebeenreducedinsizesufficientlytofitintotheperitonealcavity of smolts (ocean-ready juveniles). Secondly, thesignals emitted from these beacons are unique so thateach tagged fish can be recognized by its code, whichenables recording movement patterns and mortality ofindividual fish. This has been accomplished with twotypes of coding, pulse interval modulation or frequencyphase shifting (McMichael et al. 2010). Thirdly, auto-mated monitors have been developed that identify andrecord the passage of individual fish from the uniquesignals emitted from these beacons (Klimley et al.1998).Thecostofthese autonomousreceivershasbeenreduced sufficiently to permit the establishment of largescale arrays that can monitor salmon throughout theirmigratory cycle.These advances have led to a burst in telemetrystudies of Pacific salmon (genus Oncorhynchus).Until recently, the movements and mortality patternsof juvenile salmonids were determined by a series ofcross-shelf arrays of tag-detecting monitors that wereestablished along the continental shelf, from PointReyes in northern California to Prince William Soundin Alaska (Pacific Ocean Shelf Tracking Program -POST; Welch et al. 2002). Additionally, monitors havebeendeployedinmanyofthe estuaries and riversalongthiscoastline.CodedtagsandthePOSTarrayhavebeenused to determine the overall survival of salmon smolts