Abstract– Genetic differentiation between two reproductive ecotypes of anadromous steelhead found in the Middle Fork Eel River in northern California was tested using 16 microsatellite loci. Twelve of these loci showed significant differences in allelic frequency between the two Middle Fork Eel River steelhead populations (Fisher's exact P <0.05). Fisher's combined test for independence also supported significant genetic separation between the two reproductive ecotype (P < 0.001). Analysis of molecular variance indicated that only 1% of the overall microsatellite allelic variation contributed to differences between summer‐ and winter‐run steelhead in the Middle Fork Eel River. Variation found among individuals within the two runs equaled 18.2%. Analyses showed less genetic distance between the two populations of steelhead in the Middle Fork Eel River than in comparisons made with geographically proximate coastal winter‐run fish. Divergence time based on genetic distance for the two within‐basin reproductive ecotypes was estimated to be 16,000–28,000 years ago.

Coastal ecosystems provide numerous important ecological services, including maintenance of biodiversity and nursery grounds for many fish species of ecological and economic importance. However, human population growth has led to increased pollution, ocean warming, hypoxia, and habitat alteration that threaten ecosystem services. In this study, we used long-term datasets of fish abundance, water quality, and climatic factors to assess the threat of hypoxia and the regulating effects of climate on fish diversity and nursery conditions in Elkhorn Slough, a highly eutrophic estuary in central California (United States), which also serves as a biodiversity hot spot and critical nursery grounds for offshore fisheries in a broader region. We found that hypoxic conditions had strong negative effects on extent of suitable fish habitat, fish species richness, and abundance of the two most common flatfish species, English sole (Parophrys vetulus) and speckled sanddab (Citharichthys stigmaeus). The estuary serves as an important nursery ground for English sole, making this species vulnerable to anthropogenic threats. We determined that estuarine hypoxia was associated with significant declines in English sole nursery habitat, with cascading effects on recruitment to the offshore adult population and fishery, indicating that human land use activities can indirectly affect offshore fisheries. Estuarine hypoxic conditions varied spatially and temporally and were alleviated by strengthening of El Niño conditions through indirect pathways, a consistent result in most estuaries across the northeast Pacific. These results demonstrate that changes to coastal land use and climate can fundamentally alter the diversity and functioning of coastal nurseries and their adjacent ocean ecosystems.ecosystem services | El Niño | fisheries | hypoxia | resilience

We examined mitochondria! control-region haplotype diversity and allelic frequency distributions for three polymorphic microsatellite loci in 541 coastal Oncorhynchus mykiss collected from six habitats associated with different levels of human activity and ocean access in southern California. Extensive urbanization, climatic unpredictability, and the accelerated rate of decline in anadromous fish suggested a probable loss of genetic diversity in this area due to habitat fragmentation, geographic isolation, and population bottlenecks. Unexpectedly high levels of genetic diversity were found in southern California populations of O. mykiss. Haplotype diversity (//s) was highest in anadromous fish (H$ = 0.74) and lowest in the Whale Rock Hatchery trout (//s = 0.32). The proportion of variation attributable to population differentiation among habitat groups (Csr) was 10%. Haplotype frequencies showed a close relationship between anadromous steelhead and resident rainbow trout from closed habitats (D ST = 0.03). Combined microsatellite allelic diversity (at loci Omy77. Om\207, and Ssa289) was highest in rainbow trout from closed habitats (88%), and lowest in Whale Rock Hatchery fish (29%). Greatest microsatellite distance (8fx = 17.1) was between anadromous steelhead and reservoir rainbow trout, and closest identity (5|A = 1.8) was among rainbow trout from closed habitats, hatchery rainbow trout, and reservoir rainbow trout. Analysis of genetic distance measures for both molecular markers showed that considerations of life history patterns and freshwater habitats that retain ocean access remain important factors in the preservation of the unique genetic diversity found in southern California coastal O. mykiss.

Rainbow trout native to the McCloud River, California, USA (Oncorhynchus mykiss stonei) are thought to represent a relic, nonanadromous trout adapted to harsh, fragmented environments. These fish, commonly named McCloud River 'redband' trout, survive in their most primitive form in a small, spring-fed stream, Sheepheaven Creek, in the upper McCloud River drainage. Turn-of-the-century fisheries records document both coastal anadromous steelhead and freshwater resident trout within the McCloud River drainage. The phylogenetic position of the McCloud River redband trout within O. mykiss has been debated for over 50 years. Based on phenotypic evidence, these fish were first reported as 'southern Sierra golden trout' by Wales in 1939. Behnke (1970) considered them a relic subspecies of nonanadromous, fine-scaled trout. Allozyme and mitochondrial DNA evidence suggested a coastal lineage. In this study, we examined within- and among-basin genetic associations for Sheepheaven Creek redband trout using 11 microsatellite loci. Within-basin analyses supported unique genetic characteristics in Sheepheaven Creek's trout in comparisons with other McCloud River rainbow trout. Microsatellite data supported significant independence between Sheepheaven Creek fish and hatchery rainbow trout. Inter-basin genetic distance analyses positioned Sheepheaven Creek fish with samples collected from Lassen Creek, a geographically proximate stream containing inland redband trout. California's redband trout shared a close genetic association with Little Kern River golden trout (O.m. whitei) and isolated rainbow trout from Rio Santo Domingo, Baja, Mexico (O.m. nelsoni), suggesting a vicariant distribution of microsatellite diversity throughout the southern range of this species.

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