David G. Hankin

Genetic Analyses of Juvenile Steelhead, Coastal Cutthroat Trout, and Their Hybrids Differ Substantially from Field Identifications

Abstract Because of their similar appearance and frequent hybridization, juvenile steelhead Oncorhynchus mykiss and coastal cutthroat trout O. clarkii clarkii are difficult to distinguish visually. Nevertheless, field biologists often use visual methods to classify juvenile individuals. This study investigated hybridization between these species and determined the accuracy of field identification where hybridization occurred. Using a five-point classification system, two evaluators identified 500 fish collected from three watersheds in Humboldt County, California. Individuals were then genotyped at seven single-copy nuclear DNA genes and one mitochondrial gene, all assumed to be diagnostic for each species. Single-locus Hardy–Weinberg equilibrium, pairwise genotypic disequilibrium, and cytonuclear disequilibrium calculations revealed that subpopulations of these species were mating assortatively. Presumptive F1 hybrid individuals were rare, whereas introgressed individuals were more common. These presumpt...

Estimating Overwinter Survival of Juvenile Coho Salmon in a Northern California Stream: Accounting for Effects of Passive Integrated Transponder Tagging Mortality and Size-Dependent Survival

Abstract We used multiple resightings (live recoveries) of passive integrated transponder (PIT) tagged fish to estimate overwinter (October-March) survival rates of juvenile coho salmon Oncorhynchus kisutch in a near-pristine northern California headwater stream. Cormack-Jolly-Seber models were used to estimate period-specific survival rates and recapture probabilities from three tag groups released during October and November 1999 and March 2000. Parameter estimates from the best-supported models provided strong evidence of initial tagging mortality and also suggested that subsequent survival rates were affected by fish size at tagging. We found statistical evidence for initial PIT tagging mortality, suggested by the lower estimated period-specific survival rates for tagged fish in their first period at large compared with estimated survival rates for tagged fish that had survived through a previous period. Estimated overwinter survival rates (November-March) for fish tagged in October that were uncontam...

The Sperm Plug Is a Reliable Indicator of Mating Success in Female Dungeness Crabs, Cancer Magister

Abstract Exploitation rates for legal-sized (> 159-mm carapace width) male Dungeness crabs, Cancer magister, often reach 90% in the northern California fishery, thus making large male crabs scarce and possibly reducing mating success particularly among large (> 140-mm carapace width) female crabs. Relying on known laboratory molting and presumed mating, we characterized temporal changes in proximal sperm plugs of female C. magister from four days through 323 days following molting and mating. Although sperm plug surface area decreased steadily with increased days following mating, we found that complete sperm plugs and/or sperm plug remnants were present through approximately 180 days post mating, a period exceeding the approximately four month duration of the mating season for Dungeness crabs in northern California. Based on dissection and identification of sperm plug presence, we assessed mating success of female Dungeness crabs at two locations in northern California during June and July 1997, following the February-May mating season. Among 590 female crabs (87–167-mm carapace width) classified as having definitely molted on the basis of shell condition observations, we found that 93% had complete sperm plugs or remnants of sperm plugs in vaginal tracts. Among the 336 large (> 140 mm) definitely molted female crabs, sperm plug presence was 98.5%. Thus, despite the intense fishery on large male Dungeness crabs, sperm plug data provide evidence of essentially 100% mating success among large female crabs that molted during 1997.

Bayesian Spatial Modeling of Data from Unit-Count Surveys of Fish in Streams

Abstract We describe a framework for spatial modeling of data from surveys of stream-dwelling fish species in which repeated counts are made of animals within a sample of habitat units. Using Bayesian modeling with Markov chain-Monte Carlo (MCMC) algorithms, it is possible to estimate fish population size from repeated-count survey data while allowing fish detection probabilities to vary across the stream. We propose the use of conditional autoregressive models for modeling the spatial dependence of density across the habitat units of the stream. The spatial dependence model can be used along with covariate models for density and detection to predict density at unsampled units and thereby estimate total abundance across the stream. We apply these models to data sampled from an intensive repeated-count survey of juvenile coho salmon Oncorhynchus kisutch in McGarvey Creek, Northern California. Spatial dependence in fish density was detected, and models that account for spatial dependence produced more preci...

Hybridization between Spring- and Fall-Run Chinook Salmon Returning to the Trinity River, California

Abstract It is believed that spring- and fall-run Chinook salmon Oncorhynchus tshawytscha returning to the Trinity River, California, were once reproductively isolated such that spring-run fish spawned upstream in early fall, whereas fall-run fish spawned further downstream in late fall. However, construction of Lewiston Dam and the Trinity River Hatchery (TRH) in 1964 resulted in extensive compression of spawning habitat and the potential for inadvertent interbreeding of the two runs. In this study, we used genetic methods and developed a simulation procedure to assess the degree to which spring- and fall-run Chinook salmon returning to TRH were genetically distinct and to determine the extent of hybridization between the runs. Approximately 40 adults/week were sampled throughout the 1992 spawning season, and all individuals were genotyped at 29 polymorphic loci. Analysis with the program STRUCTURE (Pritchard et al. 2000) supported the hypothesis that the data represented two subpopulations. Individual a...

Estimating Escapement of Pacific Salmon: Marking Practices to Discriminate Wild and Hatchery Fish

Abstract Accurate discrimination between river returns of wild and hatchery anadromous Pacific salmon (Oncorhynchus spp.) is necessary if the status of the two stocks is to be monitored and if the success of hatchery mitigation programs is to be assessed. Usual hatchery management practices, including release of large numbers of unmarked fish and variable fractional marking of releases, prevent such discrimination. Many Pacific-coast salmon hatcheries presently release some fish with an adipose fin clip and a binary-coded wire tag inserted in the nasal region (AD-CWT). If a constant fraction of remaining releases carried a distinctive identifying mark, then the proportion of hatchery fish in subsequent spawning runs could be estimated. Should the majority of hatchery fish in the spawning escapement return to the hatcheries of origin, then the expected change in hatchery fish proportions between river entry and natural spawning grounds, combined with known returns to the hatcheries, may be used to estimate...

Contemporary Population Structure in Klamath River Basin Chinook Salmon Revealed by Analysis of Microsatellite Genetic Data

Abstract Chinook Salmon Oncorhynchus tshawytscha exhibit substantial population genetic structure at multiple scales. Although geography is generally more important than life history, particularly migration and run timing, for describing genetic structure in Chinook Salmon, there are several exceptions to this general pattern, and hatchery supplementation has altered natural genetic structure in some areas. Given that genetic structure of Chinook Salmon is often basin-specific, we assessed genetic variation of 27 microsatellite loci in geographically and temporally distinct natural populations and hatchery stocks in the Klamath River basin, California. Multiple analyses support recognition of three major genetic lineages from separate geographic regions in the Klamath River basin: the lower basin, the Klamath River, and the Trinity River. The lower basin group was sharply distinct, but populations in the Klamath and Trinity river lineages were connected by processes that can be described by a one-dimensio...

Decline in the Half-Pounder Life History among Trinity River, California, Steelhead

AbstractSteelhead Oncorhynchus mykiss exhibit substantial life history variation throughout their range, but the “half-pounder” life history is limited to several rivers in northern California and southern Oregon. Half-pounders first return to freshwater as immature fish after spending just 3–5 months at sea and support valuable freshwater fisheries. In the main-stem Klamath and Rogue rivers, historically and at present, half-pounder expression rates were and remain high for fall-run steelhead. We used visual classifications of the half-pounder life history from scales collected from the Trinity River to estimate half-pounder expression rates and investigate the role of size and age prior to ocean entry on the probability that adult steelhead expressed the half-pounder life history. Half-pounder expression rates among both wild and hatchery steelhead in the Trinity River have substantially declined since 1982. Among the most common age-2 wild smolt type, 71% of adults returning in 1982 had previously made...

Maintaining diversity in an artificially propagated population.

Populations may suffer unexpected loss or distortion of biodiversity as a consequence of strategies employed in artificial propagation programs. The Trinity River Fish Hatchery may have inadvertently experienced this while attempting to preserve diversity in a return time within a Chinook salmon population. We develop a model for this system and prove that the long-term distribution of return types converges and that it is strongly tied to the management strategy. Given estimates of heritabilities for return type and differential survival rates, an estimate of this long-term distribution can be computed easily.