Cottus aleuticus (coastrange sculpin) is one of two North American facultatively amphidromous sculpins, but habitat use during its planktonic larval stage is poorly documented. We analysed strontium isotopes (88Sr and 87Sr/86Sr) in otoliths of 10 adult C. aleuticus from a small coastal California stream. All showed elevated 88Sr signal intensities in the otolith core and a marine 87Sr/86Sr value in the core that rapidly shifted to and then remained at the stream value. Our results confirm a marine larval stage in this species and help explain its widespread distribution across diverse watersheds.

Objective: Debris flows are among the most extreme disturbances to streams and are predicted to become more frequent under climate change. We assessed the response of steelhead Oncorhynchus mykiss (anadromous Rainbow Trout)/Rainbow Trout (hereafter, collectively referred to as O. mykiss) ) and Coastrange Sculpin Cottus aleuticus populations to major postfire debris flows in two small coastal basins of California using noninvasive environmental DNA (eDNA) sampling. Methods: We analyzed water samples from disturbed reaches for eDNA in the first two summers after debris flows. In Big Creek, all Coastrange Sculpin habitat was disturbed by debris flows, but a major tributary occupied by O. mykiss was not affected. In Mill Creek, all available habitat for both species was disturbed. We also sampled two unburned basins as undisturbed reference streams. Result: In Big Creek, O. mykiss eDNA was detected in all water samples during both years, and concentrations in some samples approached the lowest concentrations in the reference streams. Coastrange Sculpin eDNA was detected only in a single water sample in the first year and was not detected in the second year. In Mill Creek, neither species was detected in the first year, but during the second year, O. mykiss eDNA was detected at very low concentrations in 40% of samples and Coastrange Sculpin eDNA was detected in a single sample. Conclusion: Our results indicate that O. mykiss and Coastrange Sculpins either survived in or quickly reoccupied the disturbed reaches from within the basins. However, the detection rates for cases in which all habitat for a species in a basin was affected by debris flows indicate that abundances were very low, suggesting that persistence may be uncertain unless there is successful reproduction or immigration. Finally, eDNA appears to be effective for monitoring sensitive fish populations after a major disturbance; however, detection rates in individual samples may be low and require appropriate sampling designs to achieve the desired detection probability.

Stream and riparian food webs are connected by cross-habitat exchanges of invertebrate prey that can transfer contaminants including mercury. Marine fog has been identified as a source of methylmercury (MeHg) to some terrestrial food webs in coastal California, suggesting that terrestrial invertebrates might have elevated MeHg relative to stream invertebrates and might lead to higher mercury exposure in fish that consume terrestrial subsidies. As an initial step to examine this possibility, we analyzed mercury concentrations in terrestrial and aquatic invertebrates and two fish species, steelhead/rainbow trout (Oncorhynchus mykiss) and coastrange sculpin (Cottus aleuticus), in a small watershed. Mean MeHg and total mercury (THg) concentrations in terrestrial invertebrates were three to four times higher than in aquatic invertebrates of the same trophic level. MeHg was >1000 ng/g dw in some individual centipede and scorpion samples, and also relatively high (100–300 ng/g dw) in some terrestrial detritivores, including non-native isopods. Mean THg in age 0 trout was 400 ng/g dw compared to 1200–1300 ng/g dw in age 1+ trout and sculpin, and the largest trout sampled had THg >3500 ng/g dw. However, the similar mercury concentrations between age 1+ trout and sculpin, despite different diet types, indicated that Hg concentrations in fish were not related simply to differences in consumption of terrestrial invertebrates. The high mercury concentrations we found in terrestrial invertebrates and fish suggest that further research on the sources and bioaccumulation of mercury is warranted in this region where O. mykiss populations are threatened.

Terrestrial invertebrates provide important prey subsidies to many stream fishes. Non-native invertebrates are widespread in many ecosystems, yet they have received little attention in studies of subsidies to stream food webs. We sampled coastal basins in Big Sur, California, to determine the importance of non-native isopods and other terrestrial invertebrates in the summer diet of steelhead/rainbow trout (Oncorhynchus mykiss) and to estimate the density of isopods along streambanks. Terrestrial invertebrates contributed more than 40% of the energetic value of O. mykiss stomach contents at most sites and up to 75% at some locations. Non-native isopods Armadillidium vulgare or Porcellio scaber occurred at all sites, reaching mean densities of up to 13 individuals/m(2) on streambanks, and accounted for up to 20% of the energy in the diet. The proportion of non-native isopods in the diet was positively correlated with their density at a site, and the frequency and energetic value of terrestrial invertebrates and non-native isopods in O. mykiss diets increased with fish size. In terms of the broader diet, the energetic value and taxonomic composition of stomach contents varied among sites but there was no major geographic pattern or trend to the variation, and overall O. mykiss diets were generally similar across the region. Our results highlight that non-native terrestrial invertebrates may provide a considerable but overlooked subsidy to stream fishes.

The expression of anadromy in partially migratory salmonid populations is influenced by sex-specific interactions among an individual’s genotype, condition, and environment, but genotype–phenotype relationships prior to the expression of migratory type are poorly understood. We examined whether juvenile growth and condition differed with respect to sex and a migration-associated genomic region (Omy05) in a coastal California population of steelhead and rainbow trout (Oncorhynchus mykiss). Sex and Omy05 genotype had additive effects on annual growth from age 0+ to age 1+ (∼6–18 months old), with higher growth in males and individuals with copies of the rearranged–resident haplotype. Condition at age 1+ increased with the number of copies of the rearranged–resident haplotype, with similar support for additive or interactive effects with sex; additive effects suggested that genotype differences occurred in both sexes and also that condition was slightly higher in males, while interactive effects suggested that the genotype differences occurred only in males. Our results indicate that phenotypic differences related to sex and Omy05 genotype occur well in advance of anadromous migration or freshwater maturation in this southern O. mykiss population.

AbstractAnalysis of environmental DNA (eDNA) has emerged as an important tool for investigating the occurrence and distribution of fish and other species in aquatic environments. However, in lotic systems, uncertainty remains about how environmental factors influence the downstream transport, degradation, and dilution of eDNA, and hence how detection probability varies with distance from the eDNA source. We conducted cage experiments and paired eDNA and snorkel surveys to evaluate the potential for eDNA methods to detect endangered coho salmon in Mediterranean‐climate streams of the Santa Cruz Mountains, California. Juvenile coho salmon at two densities were placed in cages, and water samples were collected and analyzed (qPCR) at seven locations from 10 to 1,000 m downstream. Although we detected coho salmon eDNA up to 1,000 m downstream of the cage, the vast majority of detections were within 200 m, and detections at greater distances occurred only at the higher fish density. In field collections from 21 stream reaches across the Santa Cruz Mountains, eDNA methods and snorkeling produced identical outcomes in terms of reach‐level detection of coho salmon. Probability of occurrence in a water sample and detection in a qPCR replicate both increased with observed fish density; however, even at the lowest densities, a protocol of three water samples and two qPCR replicates resulted in a >90% cumulative probability of detection. Overall, our studies suggest that detection probability decreased rapidly with distance in Santa Cruz Mountain streams, likely because low stream discharges, slow transport velocities, and strong interaction between the water column and stream substrate result in rapid degradation or settling of eDNA. Our findings thus support the use of eDNA methods for detecting rare species, but also indicate that local conditions strongly influence transport dynamics and hence need to be considered when developing survey designs.

Straying has been difficult to study directly in natural steelhead Oncorhynchus mykiss populations. We analyzed an opportunistic sample of seven adult steelhead from a small basin on the Big Sur coast of California to determine their life history traits, including whether they were strays. Otolith natural tags (Sr-87/Sr-86) and genetic stock identification indicated that all seven adults were strays from at least six different sources. Three adults strayed from nearby streams (<72 km) on the Big Sur coast, while three strayed from distant sources, including the Klamath River (680 km to the north); the source of one stray could not be identified. Six strays were progeny of steelhead mothers, but one was the offspring of a nonanadromous mother. Six were female and one was male, and all that could be genotyped were homozygous (n = 4) or heterozygous (n = 2) for the anadromy-associated haplotype in a migration-associated genomic region. While the opportunistic nature and small size of the sample prevents us from inferring the rate of straying into the basin, our study nonetheless demonstrates that steelhead may stray across greater distances than generally has been appreciated and that nonanadromous females can produce anadromous offspring that stray, thus providing connectivity among basins.

Diets of stream-dwelling salmonids vary at multiple spatial and temporal scales, but the relative importance of different sources of variation has rarely been evaluated for a population. In a small coastal basin in central California, we sampled diets of steelhead/Rainbow Trout Oncorhynchus mykiss monthly for a year from two reaches that differed in the presence of streambed travertine (calcium carbonate) to determine the relative magnitude of spatial, seasonal, and ontogenetic variation in consumption and diet composition. Seasonal parameters (cosine function terms for months in periodic regression and multivariate models) and fish size (FL) were greater sources of variation than differences between the two study reaches, and seasonal and ontogenetic patterns were evident despite high interindividual variability. Seasonal parameters explained the most variation in diet composition, which varied in an orderly pattern over the year. Consumption was highest in spring and summer for both aquatic and terrestrial prey, and seasonal parameters accounted for more variation than fish size for consumption of aquatic prey but this was reversed for terrestrial prey and total consumption. The main ontogenetic trend was increased consumption of terrestrial invertebrates: from 15-20% of the energy consumed by 60-100-mm fish to 60% of the energy consumed by fish larger than 160 mm. In addition, diet breadth (taxonomic richness and prey size) and the degree of variation among individuals also increased with fish size. Diet differences between sites were relatively small and included higher consumption of aquatic invertebrates at the site without travertine in 4 months and modest differences in the relative abundances of common prey taxa. Although seasonal and ontogenetic patterns were evident, interindividual variation was the dominant scale of diet variation, and diets of individual fish ranged from specialized to generalized relative to the population. Based on these findings, O. mykiss appeared to be opportunistic feeders that took advantage of diverse aquatic and terrestrial prey available in these study reaches.

Males and females often differ in their fitness optima for shared traits that have a shared genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict and protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how sexual conflict is resolved in species that lack differentiated sex chromosomes is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 55-Mb double-inversion supergene that mediates sex-specific migratory tendency through sex-dependent dominance reversal, an alternative mechanism for resolving sexual conflict. The double inversion contains key photosensory, circadian rhythm, adiposity and sex-related genes and displays a latitudinal frequency cline, indicating environmentally dependent selection. Our results show sex-dependent dominance reversal across a large autosomal supergene, a mechanism for sexual conflict resolution capable of protecting sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutations associated with typical heteromorphic sex chromosomes.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Stream and riparian food webs are connected by reciprocal fluxes of invertebrates, and a growing number of studies demonstrate strong effects of these subsidies on consumers and food webs in both habitats. However, despite its importance in understanding energy flow between these habitats, seasonality of reciprocal subsidies has been examined only in a single temperate system in Japan. We measured input of terrestrial invertebrates and emergence of adult aquatic insects for 14 months in two adjacent streams in a coastal Mediterranean basin in California to assess seasonal patterns, annual fluxes, and local variation. Fluxes of terrestrial and aquatic invertebrates fluctuated seasonally and were relatively synchronous, although in the fall of 2004, terrestrial inputs peaked 1–2 months earlier than emergence. Terrestrial inputs were similar in the two streams with annual flux of 7.9–8.6 g dry mass m−2 year−1. Emergence differed between the streams: annual emergence was 7.8 g m−2 year−1 (similar to terrestrial flux) in one reach but 5.3 g m−2 year−1 from the other. The presence of streambed travertine in the reach with lower emergence was the primary difference in habitat between the streams, suggesting that travertine may reduce emergence and alter net reciprocal flux. Comparison of our results with those from Japan suggests that seasonality and net annual flux of reciprocal stream-riparian subsidies vary among biomes due to differences in climate, vegetation, and geography. Our results also indicate that local factors, such as travertine, may cause reciprocal fluxes to vary at finer spatial scales.

Differential rates of anadromy between males and females are common in partially migratory salmonid populations, but this pattern is not fully clear for Oncorhynchus mykiss (rainbow trout/steelhead) from the limited but mixed data available. In particular, there are very few data on sex ratios of juvenile and nonanadromous (resident) fish to help assess sex composition of various life stages and life-history types. We used a recently developed Y-chromosome genetic marker to assess sex ratio of stream-dwelling (i.e., juvenile and nonanadromous) O. mykiss in a small coastal basin in central California, USA. We analysed 384 samples collected from three contiguous study reaches over 3 years. Sex ratio was 1:1 among juvenile-sized O. mykiss (< 150 mm) but highly male-skewed (83%) among nonanadromous-sized individuals (150 mm), and this sex ratio x size pattern did not differ among years or study reaches. Our results suggest that the rate of anadromy differs between males and females in this basin. Our study also demonstrates the application of new genetic markers to determine sex composition of immature and nonanadromous salmonids, which will help assess sex-specific life-history behaviour in partially migratory populations of O. mykiss and other species.

Travertine deposition occurs in streams worldwide but its effects on stream communities are poorly understood. I sampled benthic macroinvertebrates, periphyton, and reach-scale environmental variables in coastal streams in Big Sur, central California, USA, to determine the specific effects of travertine that occurred at some sites as well as to provide a broader assessment of community–habitat relationships. Total density and biomass of macroinvertebrates varied 6- and 9-fold across sites, respectively, and chlorophyll a concentrations varied 10-fold, but invertebrate and periphyton abundances were not correlated. Baetis tricaudatus (Ephemeroptera), Simuliidae (Diptera), and Chironomidae (Diptera) dominated macroinvertebrate communities across all sites, although differences in the relative abundances of these and other taxa produced moderate variation in community structure among sites (Bray-Curtis similarity coefficients of 47–84). Variation in community structure was related to a number of habitat features, notably travertine but also including variables reflecting channel morphology, flow, substrate size, and riparian tree type. Median density and biomass of macroinvertebrates were more than twice as high at sites without travertine than sites with travertine. Taxa richness also was higher at sites without travertine, and community structure differed moderately between sites with and without travertine, although there were no particular assemblages associated with either group. Non-metric multidimensional scaling (MDS) and cluster analysis of similarities in community structure appeared to separate sites with either travertine or high fines from sites without those conditions. These results demonstrate that travertine can have strong effects on stream communities, and additional studies are needed to identify the full range of effects on ecosystems and to evaluate the potential consequences of travertine for conservation efforts such as biomonitoring programs and threatened species management.

We present a statistical modeling method for estimating mortality and abundance of spawning salmon from time-series counts that eliminates the need for separate information about mortality. We model arrival and mortality using differential equations, where mortality can be constant or changing linearly, and estimate mortality and abundance from counts using maximum likelihood when multiple estimates of detection rate are available. We also develop an approximate likelihood to estimate mortality and abundance when only a single value for detection rate is available or to estimate only mortality when detection rates are entirely unknown. We demonstrate our approach using counts of coho salmon (Oncorhynchus kisutch) where mortality, abundance, and detection were determined from tagging at a weir. Our model for nonconstant mortality produced mortality estimates that closely matched the empirical data and were robust to variation in other parameters. It also provided a better fit to the stream counts and a closer abundance estimate to the weir count than the constant mortality model. Monte Carlo simulations indicated that the approximate likelihood provided reasonable estimates of mortality over most of the ranges of parameters explored, particularly under the nonconstant mortality model, and produced relatively unbiased abundance estimates using a single value for detection.

Terrestrial invertebrates are a major source of prey for salmonids in many streams. Their importance as prey appears to be related to (1) the seasonal timing of terrestrial inputs relative to the abundance of aquatic prey and (2) water temperature, which affects food demand by fish. Most studies of seasonal patterns of terrestrial inputs have come from temperate systems, and patterns in most other systems are unknown. We measured monthly biomass of aquatic invertebrates, input of terrestrial invertebrates, and diets of Oncorhynchus mykiss (non-anadromous and juvenile anadromous life history forms) for 15 months in two streams in a basin with a Mediterranean-type climate on the Big Sur coast of California. Biomass of aquatic invertebrates and terrestrial inputs followed a similar seasonal pattern; highest levels occurred in summer and early autumn and were highly correlated with water temperature. Total annual input of terrestrial invertebrates was 8.7 g(.)m(-2.)year(-1), and terrestrial inputs provided about half of the prey biomass and energy consumed by O. mykiss during the study. Normative terrestrial isopods, primarily Armadillidium vulgare, contributed 30-40% of the biomass and 20-30% of the energy consumed-the highest proportions among all taxa. The annual input, seasonal pattern, and contribution of terrestrial invertebrates to salmonids in this coastal Mediterranean-type basin were similar to published values from temperate forested streams. However, the magnitude of seasonal fluctuations of inputs was less pronounced than that in most temperate streams and appears to reflect the lower intra-annual temperature variation and longer leaf-out period in this system. Unlike many temperate streams, where terrestrial inputs provide an alternate prey source when aquatic invertebrate abundance is low, terrestrial inputs to these two coastal streams apparently provide a year-round additional source of prey that (like aquatic prey) peaks when water temperature is warmest and hence when fish growth potential is high.

Although thinning of young, even-aged forests may accelerate the development of characteristics associated with mature forests, in the short term it may negatively affect some taxa, including terrestrial salamanders. Preexisting site: conditions, including down wood, and forest management measures, such as riparian buffers, may moderate these effects, but these relationships are poorly understood. To explore whether down wood and riparian buffer widths might influence short-term responses to thinning, we sampled salamanders using ground searches before and during the first 2 years after experimental thinning at two 45- to 65-year-old headwater forest sites in western Oregon that differed in down wood volume. Prethinning distributions of terrestrial salamanders overlapped one- and two-tree height riparian buffers, and except for red-backed salamanders, overlapped very little with narrower streamside or variable-width buffers. At the site where down wood volume was low, captures of ensatina (Ensatina eschscholtzii Gray) and western red-backed salamanders (Plethodon vehiculum Cooper) both declined by 40% in thinned areas. In contrast, captures of ensatina and Oregon slender salamanders (Batrachoseps wrighti Bishop) were not significantly affected by thinning at the site where down wood volume was high. Our results suggest that site conditions, such as down wood volume, and riparian buffers may influence the effect of thinning on terrestrial salamanders, and demonstrate the tight linkage among management of aquatic, riparian, and upslope resources in headwater forests.

Wildlife-habitat relationships have been described conceptually (Morrison and others 1998) and for individual species at regional scales (Maser and others 1984; Thomas 1979; Brown 1985). Wildlife-Habitat Relationships of Oregon and Washington updates these works and provides a timely synthesis and summary of existing knowledge of wildlife-habitat relationships in these 2 states. Multi-scale habitat relationships and theory are addressed for 743 terrestrial vertebrates both in a traditional text synthesis format and in CD-ROM data matrices compiled from existing literature and expert panel assessments. This massive (736 pages and 27 chapters) book and its accompanying data reflect the collaborative efforts of over 600 participants, including 88 authors and 34 sponsors. We read this body of work cover-to-cover and put the CD-ROM to the test as part of a graduate course at Oregon State University. Our consensus of this contribution stems from numerous lively discussions, some with wildlife-habitat professionals, particularly Tom O'Neil, Mark Meyers, and Bruce Marcot. Our findings are applausive. This work provides a useful standard for description and discussion of Pacific Northwest habitats and habitat elements, develops unique conceptual themes relevant to species' habitat relationships both regionally and globally, and provides an innovative and interactive tool for information retrieval via the CD-ROM insert. Although it has some shortcomings, the book provides a lucid treatment of a broad array of wildlife subjects across multiple biomes, including temperate coniferous rainforest, shrubgrassland, and coastal-marine areas. This book serves as a foundation reference for wildlife biologists and natural resource managers attempting to understand particular habitats, wildlife species, or management contexts. This is a complex and comprehensive book, and there are too many specifics and authors to cite. Instead, we provide a summary and identify key innovations and limitations of the text. The authors derive 32 wildlife habitat types for Oregon and Washington. Cluster analysis is used to collapse species-specific cover type associations into broad "habitat types" based on similarity of associated wildlife species groups (Chapter 1). This is a satisfying approach in that multi-species data on distribution patterns are used to determine the broad scale habitat types, as opposed to subjectively defining categories. The resulting habitats are characterized (Chapter 2, >30 p color photographs; Chapter 5, Tables 1 to 3) and mapped across Oregon and Washington (pp vii-xi). In addition, habitat heterogeneity is acknowledged by a summary of natural disturbance regimes, succession dynamics, and management impacts. We anticipate that Chapter 2 will be frequently cited to provide basic habitat descriptions. We identified 2 issues of concern in the formulation and presentation of the broad habitat types. First, we noted that the initial vegetative cover associations used in the cluster analysis