For several decades, annually recurring blooms of the photosynthetic ciliate Myrionecta rubra have been observed in the Columbia River estuary in late summer. In an effort to understand the dynamics of these blooms, we investigated the genetic variability of M. rubra and its cryptophyte plastids within 3 large estuarine blooms formed in consecutive years (2007 to 2009), and conducted a broader spatial survey along the coasts of Oregon and Washington. Analysis of the '18S-28S' sequences specific for Mesodiniidae uncovered at least 5 variants of M. rubra within the Columbia River coastal margin in spring and summer, but only one of these M. rubra variants was implicated in estuary bloom formation. Using a multigene approach, we show that the bloom-forming variant of M. rubra appears to harbor the same cryptophyte chloroplast in recurring blooms. Analyses of chloroplast 16S rRNA, cryptophyte RuBisCO and Photosystem II D2 genes together suggest that the plastid is derived from Teleaulax amphioxeia. Free-living cells of this species and of other cryptophytes were practically absent from the bloom patches in the estuary main channels based on 18S rDNA sequence analyses. The respectively low and high proportions of T. amphioxeia nuclei and chloroplast signals found in the M. rubra bloom of the Columbia River estuary in successive years supports the notion of an association (either endosymbiosis or kleptoplastidy) between T. amphioxeia and the bloom-forming M. rubra variant, with loss of cryptophyte nuclei. The genetic variability of M. rubra uncovered here is relevant to the controversy in the literature regarding the cryptophyte/M. rubra association.

We monitored fish assemblages monthly at estuarine and tidal freshwater sites in the lower Columbia River and estuary from January 2002 through September 2007 in order to identify specific salmon stocks and migration stages that may benefit from habitat restoration initiatives. We report landscape‐scale and seasonal variation in abundance, size, hatchery production (based on adipose fin clips), and genetic stock of origin of juvenile Chinook salmon Oncorhynchus tshawytscha. From fish implanted with coded wire tags (CWTs), we also determined the sites of release and inferred migration patterns. Chinook salmon were found in diverse life history stages and forms, including fry migrants, fingerlings, and (fewer) yearlings. Abundance increased in February and decreased in August, but salmon were present in all months each year. Spatial gradients in abundance and size were strong, with fewer but larger fish in brackish than in tidal freshwater zones. Overall, 30% of the Chinook salmon measured were fry (≤60 mm) that were likely naturally produced fish. These occurred at higher mean monthly proportions in tidal freshwater than in estuarine zones. In contrast, most larger fish were probably raised in hatcheries. Genetic stock assessment revealed that the majority of the Chinook salmon analyzed were from fall‐run stock groups originating in the lower Columbia River, with 15% originating from other stock groups. Of these minority contributors, about 6% were identified as upper Columbia River summer–fall‐run Chinook salmon while seven other stock groups accounted for the remainder, including 3% from transplants originating in southern Oregon's Rogue River. Recaptures of tagged fish revealed maximum migration times of 143 d for subyearlings and 52 d for yearlings, and both CWT and genetic data indicated that fall Chinook salmon from coastal rivers occasionally entered the estuary. These data demonstrated a widespread temporal and spatial distribution of subyearling Chinook salmon in shallow‐water habitats of the lower Columbia River and estuary. Received June 28, 2011; accepted February 28, 2012

Ecologists have long debated the relative importance of biotic interactions vs. abiotic forces on the population dynamics of both marine and terrestrial organisms. Investigation of stock size in Dungeness crab (Cancer magister) is a classic example of this debate. We first tested the hypothesis that adult population size was set by larval success. We found that during a five-year sampling period, adult crab population size from Oregon through central California, USA, as measured by the commercial catch, varied directly with the number of terminal-stage larvae (megalopae) returning to Coos Bay, Oregon, four years earlier; adult population size was largely determined (> 90% of the variation) by success during the larval stage. We then tested whether biotic interactions or abiotic forces caused the variation in larval success. Most of the variation (> 90%) in the number of returning megalopae is explained by the timing of the spring transition, a seasonal shift in atmospheric forcing that drives ocean currents along the west coast of the United States. Early spring transitions lead to larger numbers of returning Dungeness megalopae, while in four other crab taxa, species with very different life history characteristics, early-spring transitions lead to lower numbers of returning megalopae. During the past roughly 30 years, the size of the commercial catch of Dungeness crab is significantly and negatively correlated with the date of the spring transition throughout the California Current system. Long-term variation in the date of the spring transition may explain a major crash in the Dungeness crab fishery in central California, which began in the late 1950s. The data suggest that Dungeness crab population size is determined by variation in larval success and that a significant portion of this variation is due to the timing of the spring transition, a large-scale climatic forcer.