Joseph D. Kiernan’s research while affiliated with University of California, Santa Cruz and other places

Recent work has revealed the importance of contemporary evolution in shaping ecological outcomes. In particular, rapid evolutionary divergence between populations has been shown to impact the ecology of populations, communities, and ecosystems. While studies have focused largely on the role of adaptive divergence in generating ecologically important variation among populations, much less is known about the role of gene flow in shaping ecological outcomes. After divergence, populations may continue to interact through gene flow, which may influence evolutionary and ecological processes. Here, we investigate the role of gene flow in shaping the contemporary evolution and ecology of recently diverged populations of anadromous steelhead and resident rainbow trout (Oncorhynchus mykiss). Results show that resident rainbow trout introduced above waterfalls have diverged evolutionarily from downstream anadromous steelhead, which were the source of introductions. However, the movement of fish from above to below the waterfalls has facilitated gene flow, which has reshaped genetic and phenotypic variation in the anadromous source population. In particular, gene flow has led to an increased frequency of residency, which in turn has altered population density, size structure, and sex ratio. This result establishes gene flow as a contemporary evolutionary process that can have important ecological outcomes. From a management perspective, anadromous steelhead are generally regarded as a higher conservation priority than resident rainbow trout, even when found within the same watershed. Our results show that anadromous and resident O. mykiss populations may be connected via gene flow, with important ecological consequences. Such eco‐evolutionary processes should be considered when managing recently diverged populations connected by gene flow.

Stream restorations are increasingly critical for managing and recovering freshwater biodiversity in human‐dominated landscapes. However, few studies have quantified how rehabilitative actions promulgate through aquatic communities over decades. Here, a long‐term dataset is analyzed for fish assemblage change, incorporating data pre‐ and post‐restoration periods, and testing the extent to which native assemblage stability has increased over time. In the late 1950s, a large capacity dam was installed on Putah Creek (Solano County, CA, USA), which altered the natural flow regime, channel structure, geomorphic processes, and overall ecological function. Notably, downstream flows were reduced (especially during summer months) resulting in an aquatic assemblage dominated by warm‐water nonnative species, while endemic native species subsisted at low levels as subordinates. A court‐mediated Accord was ratified in 2000, providing a more natural flow regime, specifically for native and anadromous fishes in the stream. The richness of nonnative species decreased at every site following the Accord, while the richness of native species increased or stayed constant. At the three most upstream sites, native species richness increased over time and ultimately exceeded nonnative richness. Native assemblage recovery was strongest upriver, closer to flow releases and habitat restoration activities, and decreased longitudinally downstream. Rank–abundance curves through time revealed that, while species evenness was low throughout the study, dominance shifted from nonnative to native species in the upstream sites coincident with rehabilitation efforts. Mean rank shifts decreased following flow rehabilitation; thus the assemblage became increasingly stable over time following flow rehabilitation. Putah Creek's rehabilitation may represent a model for others interested in improving endemic freshwater communities in degraded ecosystems.

A greater understanding of eDNA behavior in the environment is needed before it can be employed for ecosystem monitoring applications. The objectives of this study were to use autonomous sampling to conduct long‐term, high‐frequency monitoring of the eDNA of native salmonid species in a Californian coastal stream, describe temporal variation of eDNA on multiple scales and identify environmental factors that drive this variation, and evaluate the ability of the eDNA datasets to detect rare species and represent organismal abundance. Using high‐throughput autonomous environmental sample processors (ESPs) and qPCR, we enumerated eDNA concentrations from 674 water samples collected at subdaily intervals over 360 days at a single site. We detected eDNA from two imperiled salmonids (coho salmon Oncorhynchus kisutch and steelhead/rainbow trout O. mykiss) in most samples; O. kisutch eDNA was generally in lower concentration and more variable than O. mykiss eDNA. High‐frequency (i.e., subdaily and daily) variability in salmonid eDNA concentrations showed occasional patchiness (i.e., large differences between consecutive samples), while seasonal differences were observed consistent with the ecology of the species at this site. Salmonid eDNA concentrations were significantly associated with creek discharge, photoperiod, and whether the creek mouth was open or closed by a seasonal sandbar. The release of hatchery‐origin O. kisutch parr into the stream was associated with a significant increase in eDNA concentration for the remainder of the study. We compared eDNA signals with fish abundance data collected from traps located at the site. Fish were detected more often by eDNA than from trapping. Significant positive associations between fish abundance and eDNA concentrations were observed for O. mykiss; however, no such associations were observed for O. kisutch. This study adds to our knowledge on the occurrence and behavior of fish eDNA in lotic systems and informs future biomonitoring efforts using automated sampling technology. The objective of our study was to conduct high‐frequency autonomous sampling of salmonid eDNA in a coastal stream, elucidate the temporal patterns and environmental correlates of the eDNA signal, and compare the signal with a measure of abundance obtained from a fish trap collocated at the study site. We sampled one to three times per day for approximately one year, collecting nearly 700 samples. The eDNA signals showed high variability on short time scales and were aligned with expected salmonid seasonal trends in this ecosystem. Salmonid eDNA was significantly associated with creek discharge, photoperiod, and whether the creek mouth was open or closed by a seasonal sandbar. Comparing eDNA with fish counts from traps, we found that eDNA detected fish more often than traps but that eDNA concentrations were weakly or not at all correlated with fish abundance.

In California (USA), seasonal lagoons provide important oversummer rearing habitat for juvenile steelhead trout (anadromous Oncorhynchus mykiss ). However, key water quality parameters such as temperature and dissolved oxygen concentration can periodically approach or exceed the physiological tolerances of steelhead during the protracted dry season. A field study employing distributed temperature sensing technology, water quality monitoring, habitat mapping, and mark-recapture sampling was conducted to examine how shifting environmental conditions affected the performance and behavior of juvenile steelhead in the Scott Creek estuary/lagoon (Santa Cruz County). Abiotic conditions were driven by episodic inputs of seawater to the typically freshwater lagoon. During midsummer, the water column was vertically stratified which reduced suitable lagoon rearing habitat by approximately 40%. Nevertheless, steelhead abundance, growth, and condition factor were high during the summer and decreased in autumn following lagoon destratification and cooling. Unlike previous work, this study identified limited emigration from the lagoon to riverine habitat during the summer. Instead, juvenile steelhead exhibited crepuscular movement patterns within the lagoon, with peaks in upstream (to upper lagoon habitat) and downstream (to lower lagoon habitat) movement occurring at dawn and dusk, respectively. This study underscores that habitat complexity and connectivity are critical for juvenile steelhead production and persistence and provides insight into steelhead habitat use and behavior in seasonal lagoons.

Natural selection shapes the evolution of antipredator traits in prey. However, selection in the wild depends on ecological context, including features of predator and prey populations, making field studies of selection critical to understanding how predators shape selection on prey defences. Threespine stickleback (Gasterosteus aculeatus) is a classic system to study the effects of predators on the natural selection of prey. In lakes and rivers, fish predators have been shown to impose selection against low plated adult stickleback phenotypes and genotypes. We directly measured selection by predatory salmonids on the Ectodysplasin‐A (Eda) gene in estuary stickleback from California. Despite previous studies showing a positive correlation between predator presence and frequency of the Eda “complete” allele in estuary populations, we found that Eda “low” genotypes were not significantly more frequent in salmonid predator diets. Further, we found no evidence of changes in Eda genotype frequencies across generations that would suggest directional selection driven by predators. Prior selection studies have examined the effects of large resident trout on adult stickleback. In contrast, predators in this study were juvenile anadromous salmonids, which only ate juvenile stickleback whose plate phenotypes had not fully developed. Thus, in this case, predator life history and stickleback ontogeny may preclude strong selection on stickleback armour. Our results underscore the importance of selection studies in the wild for understanding the context‐dependent nature of selection in natural populations.

Conservation efforts for Pacific salmon (Oncorhynchus spp.) increasingly prioritize maintenance of cool water temperatures that protect all freshwater life stages. However, development of appropriate temperature standards requires a robust understanding of the interactions among water temperature, ecosystem productivity, and fish performance. We used a series of in situ enclosures to examine how natural spatiotemporal gradients in thermal conditions and prey availability affected the summer growth and survival of age-0+ coho salmon (Oncorhynchus kisutch). Coho salmon absolute growth rates peaked at a mean daily average water temperature (mean T) of 16.6 °C and an associated maximum weekly maximum temperature (MWMT) of 21.1 °C. Juvenile growth under these thermal conditions was sixfold greater than the growth rates observed for conspecifics rearing in the coolest study reach (mean T = 13.0 °C; MWMT = 16.0 °C). Even at the highest rearing temperature (mean T = 18.1 °C; MWMT = 24.0 °C), growth rates remained positive and above the study-wide average, although overall survival was reduced. Among the predictor variables examined, invertebrate prey abundance was the predominant factor influencing age-0+ coho salmon growth. These results suggest that abundant prey resources may mitigate the negative effects of elevated water temperature on fish growth in riverine environments. Given the likelihood of increasing stream temperatures with climate change, productive ecosystems may provide critical refuges for juvenile salmonids.

The California Coastal Monitoring Plan (CMP; Adams et al. 2011) advocates a two-stage approach (i.e., redd counts and fixed counting/trapping stations) to estimate adult salmonid abundance in the northern monitoring area (Figure 1). Redd counts often fail to produce robust estimates of abundance for coho salmon and steelhead in watersheds at the southern end of the Central California Coast (CCC) ESU/DPS for two reason: 1. Sandbars form across creek mouths each summer and persist until large winter storms produce sufficient streamflow to erode the sandbar (Figure 2A,B). Once the sandbar is opened, adult coho salmon and steelhead often concurrently move into the stream and begin spawning (Table 1, Figure 2C). 2. Redds are most often encountered after construction without live fish or carcasses in the immediate vicinity. Hence, definitive species assignments are often not possible (Figure 3). To address the uncertainty surrounding redds of unknown origin, two species assignment methods are frequently applied in support of the CMP: • A logistic regression model that makes species predictions based on the timing of redd construction and redd geometry (Gallagher & Gallagher 2005, hereinafter G&G). • The k-nearest neighbors (kNN) algorithm which assigns species based on a majority rule of known nearest neighbors in time and space (Ricker et al. 2014). The relative performance of these methods, and their applicability to watersheds at the southern end of the CCC ESU/DPS, remain poorly understood

Over the last three decades, passive integrated transponder (PIT) tags have been widely used to study fish populations. Interpretation of PIT tag detections, however, can be confounded by the presence of ghost tags, tags liberated when a fish dies. We used a combination of mobile antenna surveys, stationary antenna detections, and multistate mark–recapture modeling to assess the abundance and fate of ghost tags in a coastal California watershed. Accumulation of ghost tags from released hatchery-origin coho salmon (Oncorhynchus kisutch) smolts was substantial during California’s recent drought, with 2224 ghost tags identified during mobile reader surveys. Between surveys, PIT tags moved downstream a median distance of 346 m and a maximum distance of 1982 m. Stationary antenna array detections indicated that these movements occurred during high-flow events, concurrent with live fish movement. The multistate model estimated that, during winter, approximately 40% of tags were buried in the substrate beyond the read range of mobile readers. Failure to account for transport and burial dynamics of ghost tags can lead to biased estimates of fish abundance, survival, and movement.

We investigated how extreme drought conditions influenced the abundance, growth, movement, and seawater readiness of juvenile coho salmon (Oncorhynchus kisutch) and steelhead trout (Oncorhynchus mykiss) in a small central California coastal lagoon. In 2015, the seasonal sandbar at the mouth of Scott Creek formed over 2 months earlier than average, effectively trapping fish in the lagoon for 7 additional months (mid-May through December) before outmigration opportunities eventually resumed. Monthly mark–recapture sampling demonstrated that juvenile coho salmon and steelhead were able to persist in the lagoon during extended periods of high water temperature and low dissolved oxygen concentration. Both salmonid species exhibited similar temporal trends in abundance, growth, and Na⁺-K⁺-ATPase activity levels during lagoon residence; however, abundance and growth rates were consistently higher for steelhead. Stationary passive integrated transponder tag antenna detections revealed recurrent movement of individuals between the warm lagoon and cooler lower mainstem creek, suggesting individuals regulated key physiological processes by moving between the adjacent habitats. Our study provides new insight concerning the consequences of drought for imperiled salmonid populations and underscores the importance of life-history diversity during extreme climatic events.

Dam removal is often proposed for restoration of anadromous salmonid populations, which are in serious decline in California. However, the benefits of dam removal vary due to differences in affected populations and potential for environmental impacts. Here, we develop an assessment method to examine the relationship between dam removal and salmonid conservation, focusing on dams that act as complete migration barriers. Specifically, we (1) review the effects of dams on anadromous salmonids, (2) describe factors specific to dam removal in California, (3) propose a method to evaluate dam removal effects on salmonids, (4) apply this method to evaluate 24 dams, and (5) discuss potential effects of removing four dams on the Klamath River. Our flexible rating system can rapidly assess the likely effects of dam removal, as a first step in the prioritization of multiple dam removals. We rated eight dams proposed for removal and compared them with another 16 dams, which are not candidates for removal. Twelve of the 24 dams evaluated had scores that indicated at least a moderate benefit to salmonids following removal. In particular, scores indicated that removal of the four dams on the Klamath River is warranted for salmonid conservation. Ultimately, all dams will be abandoned, removed, or rebuilt even if the timespan is hundreds of years. Thus, periodic evaluation of the environmental benefits of dam removal is needed using criteria such as those presented in this paper.