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Yoichiro Kanno

Publications and source records attributed to Yoichiro Kanno.

At least 19 recordsLinked to original sources
USGS2026

A multi-species, multi-season evaluation of body condition effects on fish survival in a coolwater stream

Objective Body condition is often used as a surrogate of individual fitness in fisheries ecology and management, but empirical data demonstrating this linkage are few. Here, we investigated whether weight at length (i.e., body condition) explained individual variation in survival. Methods We conducted a mark–recapture survey of three native fishes subseasonally (every 2 months) over 28 months in a coolwater Piedmont stream in South Carolina, United States. We used a Cormack–Jolly–Seber model in the Bayesian state–space framework to characterize whether survival was explained by body condition. Results Body condition changed subseasonally, with its peak in spring (May) and trough in fall (November) in all three species (Bluehead Chub Nocomis leptocephalus , Creek Chub Semotilus atromaculatus , and Mottled Sculpin Cottus bairdii ). Survival decreased in warmer subseasons for all species. Additionally, individuals with higher body condition survived better than those with lower condition only in these warmer subseasons and only in the Mottled Sculpin, a species that is territorial and the most intolerant of warmer temperatures among the study species. Conclusions Our findings show that body condition is a predictor of survival only when populations undergo high mortalities in some but not all species, which are likely caused by a combination of factors, such as physiological stress, diminished food resources, and increased competition for resources.

South Carolina↗
USGS2025

Riverscape genetics of nonnative Brook Trout to inform native cutthroat trout conservation

Objective Understanding how riverscape features influence gene flow is critical for managing population connectivity in freshwater species. We examined how landscape and stream characteristics shape the spatial genetic structure of nonnative Brook Trout Salvelinus fontinalis in a headwater stream network proposed for reintroduction of federally threatened Greenback Cutthroat Trout Oncorhynchus virginalis stomias . Brook Trout were studied to evaluate the suitability of this habitat for supporting a native trout metapopulation. Methods We genotyped 757 Brook Trout from 22 sites across a 60-km stream network using 12 microsatellite loci. Spatial genetic structure was assessed using clustering analysis (program STRUCTURE) and pairwise differentiation metrics ( F ST and Jost’s D ). A spatial network modeling approach was used to quantify the effects of riverscape features (e.g., stream gradient, stream order, waterfalls, and flow direction) on trout gene flow. Results Genetic clustering identified four distinct tributary groups, while estimates of pairwise genetic differentiation indicated some genetic connectivity across the network (mean F ST = 0.04; mean Jost’s D = 0.06). Trout gene flow was impeded by waterfalls, steep stream gradients, and increased hydrologic distance. Higher stream order and downstream flow direction were associated with stronger gene flow, and stream segments containing waterfalls and steeper gradients showed greater asymmetries between upstream and downstream gene flow. Conclusions Brook Trout populations in this stream network are spatially structured, but gene flow persists and is mediated by physical riverscape features and hydrologic distance. The observed patterns of genetic connectivity suggest that this habitat can support connectivity among populations of reintroduced Greenback Cutthroat Trout. In future native trout reintroduction efforts, prioritizing habitats with gradual stream gradients and fewer waterfalls would promote population connectivity.

Transactions of the American Fisheries Society↗
USGS2025

Integrated analysis of marked and count data to characterizefine-scale stream fish movement

Immigration and emigration are key demographic processes of animal population dynamics. However, 3 we have limited knowledge on how fine-scale movement varies over space and time. We developed a 4 Bayesian integrated population model using individual mark-recapture and count data to characterize 5 fine-scale movement of stream fish at 20-m resolution every two months for 28 months. Our study 6 targeted small-bodied fish, for which imperfect capture was accounted for (bluehead chub Nocomis 7 leptocephalus, creek chub Semotilus atromaculatus and mottled sculpin Cottus bairdii). Based on 8 data from 2,021 individuals across all species, we found that proportions of immigrants averaged 9 30-42% among the study species, but they varied over space and time. Creek chub immigrants 10 increased during warmer intervals when individuals grew more and transitioned between body size 11 classes, suggesting that immigration was due to ontogenetic habitat shifts. There was a weak pattern 12 across the species that individuals were more likely to leave 20-m sections when flow was higher. 13 Water-column species (bluehead chub and creek chub) were more likely to immigrate into and stay 14 in deeper sections with more pool area. Across all species and occasions, number of immigrants 15 to stream sections did not decrease with number of individuals that survived and stayed in the 16 same sections. Thus, the habitat did not appear saturated, and our data provided no evidence that 17 intra-specific interactions affected fine-scale movement at our fish densities. In conclusion, high 18 turnover rates characterized fish movement among stream sections and their variation was associated 19 with temporal and spatial shifts in abiotic conditions.

South Carolina↗
USGS2024

A genetic assessment of natural barriers for isolating a habitat network proposed for Greenback Cutthroat Trout reintroduction

Objective: Native inland trout conservation efforts rely on physical barriers to exclude nonnative salmonids from target habitats. We used genetic techniques to evaluate a series of natural waterfalls for their potential to serve as barriers to prevent nonnative salmonids from entering a proposed reintroduction area for federally threatened Greenback Cutthroat Trout Oncorhynchus virginalis stomias . Methods: Genetic samples were collected from nonnative Brook Trout Salvelinus fontinalis at 11 sampling reaches above and below natural waterfalls (height: ~1–3 m under base flow conditions) along a 33-km segment of Colorado's upper Cache la Poudre River near the outflow of the proposed reintroduction area. To evaluate whether upstream movement of Brook Trout is restricted by any of these waterfalls, we characterized longitudinal trends in genetic diversity along the river corridor and examined patterns of genetic differentiation and population structure in relation to waterfall locations using a panel of microsatellites. Result: We found no evidence that the waterfalls served as complete movement barriers for nonnative Brook Trout based on genetic clustering analyses, estimates of population differentiation, and longitudinal genetic patterns. Our multilocus assessment did not identify alleles restricted to downstream reaches, and the river segment was genetically homogenized. Conclusion: Our evaluation suggests that the existing waterfalls do not fully prevent upstream movement by nonnative Brook Trout, and thus barrier modification would be needed to establish an isolated Greenback Cutthroat Trout population in the proposed wilderness area.

Colorado↗
USGS2024

The past, present, and a future for native charr in Japan

Charrs ( Salvelinus ) reach their southernmost distribution in Japan, and are uniquely adapted to the short, steep streams of this island archipelago. Southern Asian Dolly Varden ( Salvelinus curilus ) occur only in Hokkaido Island, whereas white-spotted charr ( Salvelinus leucomaenis ) range to southern Honshu. Both species diverged from an ancestral lineage during the late Pliocene/early Pleistocene, when lowered sea levels created semi-enclosed water bodies in the seas of Japan and Okhotsk. Genetic analyses showed S. curilus represents the most ancient divergence from the Dolly Varden ( Salvelinus malma ) - Arctic charr ( Salvelinus alpinus ) group, and revealed five lineages of S. leucomaenis which align differently than traditional subspecies. Japanese charr display diverse and flexible life histories including anadromous fish with partial migration, and fluvial, adfluvial, and resident forms. In Hokkaido, Dolly Varden are distributed upstream and white-spotted charr downstream. They coexist in narrow sympatric zones through adaptive shifts by Dolly Varden in behavior and morphology that facilitate benthic foraging. Both species hybridize with native and nonnative salmonids, and are displaced from microhabitats and decline in abundance when rainbow trout ( Oncorhynchus mykiss ) and brown trout ( Salmo trutta ) invade. Japan streams contain over 95,000 erosion control dams which create short stream fragments (medians ~200 m). This has increased extirpation of charr populations via lower genetic diversity and stochastic and demographic factors. Tributaries provide complex rearing habitats, afford refuges from floods, and supply recruits that sustain populations in mainstem fragments and create metapopulations in connected riverscapes. Charr play central roles in linked stream-riparian food webs, and cause direct and indirect effects that cascade to streambed algae and riparian predators when linkages are disrupted by anthropogenic effects or altered by native parasites. Many charr populations are threatened by habitat fragmentation and introgression or invasion by nonnative forms, but efforts to conserve charr are growing. These include restoring connectivity among pure populations above barriers that prevent invasions, protecting tributary nurseries, and instituting angling regulations to protect headwater populations. Key steps include inventorying pure populations, identifying conservation units, selecting appropriate management based on connectivity and biotic interactions, and engaging stakeholders and youth to engender an ethic for conserving irreplaceable charr lineages.

Ichthyological Research↗
USGS2023

Aging contrast: A contrastive learning framework for fish re-identification across seasons and years.

The fields of biology, ecology, and fisheries management are witnessing a growing demand for distinguishing individual fish. In recent years, deep learning methods have emerged as a promising tool for image-based fish recognition. Our study is focused on the re-identification of masu salmon from Japan, wherein fish were individually marked and photographed to evaluate discriminative body characteristics. Unlike previous studies where fish were sampled during the same time period, we evaluated individual re-identification across seasons and years to address challenges due to aging, seasonal variation, and other factors. In this paper, we propose a new contrastive learning framework called Ag ing Co ntrast (AgCo) and evaluate its performance on the masu salmon dataset. Our analysis indicates that, unlike large changes in body size over time, the pattern of parr marks on the lateral line of the fish body remains relatively stable, despite some change in coloration across seasons. AgCo accounts for such seasonally-invariant features and performs re-identification based on the cosine similarity of these features. Extensive experiments show that our AgCo method outperforms other state-of-the-art methods.

Conference Paper↗
USGS2023

Spatial asynchrony and cross-scale climate interactions in populations of a coldwater stream fish

Climate change affects populations over broad geographic ranges due to spatially autocorrelated abiotic conditions known as the Moran effect. However, populations do not always respond to broad-scale environmental changes synchronously across a landscape. We combined multiple datasets for a retrospective analysis of time-series count data (5–28 annual samples per segment) at 144 stream segments dispersed over nearly 1,000 linear kilometers of range to characterize the population structure and scale of spatial synchrony across the southern native range of a coldwater stream fish (brook trout, Salvelinus fontinalis ), which is sensitive to stream temperature and flow variations. Spatial synchrony differed by life stage and geographic region: it was stronger in the juvenile life stage than in the adult life stage and in the northern sub-region than in the southern sub-region. Spatial synchrony of trout populations extended to 100–200 km but was much weaker than that of climate variables such as temperature, precipitation, and stream flow. Early life stage abundance changed over time due to annual variation in summer temperature and winter and spring stream flow conditions. Climate effects on abundance differed between sub-regions and among local populations within sub-regions, indicating multiple cross-scale interactions where climate interacted with local habitat to generate only a modest pattern of population synchrony over space. Overall, our analysis showed higher degrees of response heterogeneity of local populations to climate variation and consequently population asynchrony than previously shown based on analysis of individual, geographically restricted datasets. This response heterogeneity indicates that certain local segments characterized by population asynchrony and resistance to climate variation could represent unique populations of this iconic native coldwater fish that warrant targeted conservation. Advancing the conservation of this species can include actions that identify such priority populations and incorporate them into landscape-level conservation planning. Our approach is applicable to other widespread aquatic species sensitive to climate change.

Global Change Biology↗
USGS2023

Climate change impacts on native cutthroat trout habitat in Colorado streams

Headwater streams support vital aquatic habitat yet are vulnerable to changing climate due to their high elevation and small size. Coldwater fish are especially sensitive to the altered streamflow and water temperature regimes during summer low flow periods. Though previous studies have provided insights on how changes in climate and alterations in stream discharge may affect habitat availability for various native cutthroat trout species, suitable physical habitats have not been evaluated under future climate projections for the threatened Greenback Cutthroat Trout (GBCT) native to headwater regions of Colorado, USA. Thus, this study used field data collected from selected headwater streams across the current distribution of GBCT to construct one-dimensional hydraulic models to evaluate streamflow and physical habitat under four future climate projections. Results illustrate reductions in both predicted streamflow and physical habitat for all future climate projections across study sites. The projected mean summer streamflow shows greater decline (−52% on average) compared to the projected decline in mean August flow (−21% on average). Moreover, sites located at a relative higher elevation with larger substrate and steeper slope were projected to experience more reductions in physical habitat due to streamflow reductions. Specifically, streams with step-pool morphologies may experience grater changes in available habitat compared to pool-riffle streams. Future climate change studies related to coldwater fish that examine spatial variation in flow alteration could provide novel data to complement the existing literature on the thermal characteristics. Tailoring reintroduction and management efforts for GBCT to the individual headwater stream with adequate on-site monitoring could provide a more holistic conservation approach.

Colorado↗
USGS2022

Simple statistical models can be sufficient for testing hypotheses with population time series data

Time-series data offer wide-ranging opportunities to test hypotheses about the physical and biological factors that influence species abundances. Although sophisticated models have been developed and applied to analyze abundance time series, they require information about species detectability that is often unavailable. We propose that in many cases, simpler models are adequate for testing hypotheses. We consider three relatively simple regression models for time series, using simulated and empirical (fish and mammal) datasets. Model A is a conventional generalized linear model of abundance, model B adds a temporal autoregressive term, and model C uses an estimate of population growth rate as a response variable, with the option of including a term for density dependence. All models can be fit using Bayesian and non-Bayesian methods. Simulation results demonstrated that model C tended to have greater support for long-lived, lower-fecundity organisms (K life-history strategists), while model A, the simplest, tended to be supported for shorter-lived, high-fecundity organisms (r life-history strategists). Analysis of real-world fish and mammal datasets found that models A, B, and C each enjoyed support for at least some species, but sometimes yielded different insights. In particular, model C indicated effects of predictor variables that were not evident in analyses with models A and B. Bayesian and frequentist models yielded similar parameter estimates and performance. We conclude that relatively simple models are useful for testing hypotheses about the factors that influence abundance in time-series data, and can be appropriate choices for datasets that lack the information needed to fit more complicated models. When feasible, we advise fitting datasets with multiple models because they can provide complementary information.

Ecology and Evolution↗
USGS2022

Population genetics reveals bidirectional fish movement across the Continental Divide via an interbasin water transfer

Interbasin water transfers are becoming an increasingly common tool to satisfy municipal and agricultural water demand, but their impacts on movement and gene flow of aquatic organisms are poorly understood. The Grand Ditch is an interbasin water transfer that diverts water from tributaries of the upper Colorado River on the west side of the Continental Divide to the upper Cache la Poudre River on the east side of the Continental Divide. We used single nucleotide polymorphisms to characterize population genetic structure in cutthroat trout ( Oncorhynchus clarkii ) and determine if fish utilize the Grand Ditch as a movement corridor. Samples were collected from two sites on the west side and three sites on the east side of the Continental Divide. We identified two or three genetic clusters, and relative migration rates and spatial distributions of admixed individuals indicated that the Grand Ditch facilitated bidirectional fish movement across the Continental Divide, a major biogeographic barrier. Previous studies have demonstrated ecological impacts of interbasin water transfers, but our study is one of the first to use genetics to understand how interbasin water transfers affect connectivity between previously isolated watersheds. We also discuss implications on native trout management and balancing water demand and biodiversity conservation.

Colorado↗
USGS2022

Toward improved prediction of streamflow effects on freshwater fishes

Understanding the effects of hydrology on fish populations is essential to managing for native fish conservation. However, despite decades of research illustrating streamflow influences on fish habitat, reproduction and survival, biologists remain challenged when tasked with predicting how fish populations will respond to changes in flow regimes. This uncertainty stems from insufficient understanding of the context-dependent mechanisms underlying fish responses to, for example, periods of reduced flow or altered frequency of high-flow events. We aim to address this gap by drawing on previous research to hypothesize mechanisms by which low- and high-flows influence fish populations and communities, identifying challenges that stem from data limitations and ecological complexity, and outlining research directions that can advance an empirical basis for prediction. Focusing flow-ecology research on testing and refining mechanistic hypotheses can help narrow management uncertainties and better support species conservation in changing flow regimes.

Fisheries Magazine↗
USGS2022

Gene flow and spatial population structure of Brook Trout in a large headwater stream network in Colorado

We studied gene flow of non-native Brook Trout Salvelinus fontinalis in a 60-km section of continuous stream network in the upper Cache la Poudre River basin, where a large-scale reclamation effort to restore federally threatened Greenback Cutthroat Trout Oncorhynchus clarkii stomias (GBCT) is taking place. This effort—the Poudre Headwaters Project—represents the most important recovery effort of the state fish of Colorado and could result in a fivefold increase in total occupied GBCT habitat. However, the reclamation area is currently dominated by non-native Brook Trout; key steps to ensure the success of the Poudre Headwaters Project include removing non-native Brook Trout and physically isolating the area from reinvasion. We examined existing genetic population structure in the reclamation area to provide science-based guidance for effective Brook Trout removal and subsequent GBCT reintroduction. During 2018 and 2019, tissue samples were collected from 23 sites in the Long Draw region. We genotyped 792 Brook Trout using 12 microsatellite loci to examine genetic population structure within the reclamation area. Our results show that fine-scale genetic population structure is present among sites (F ST = 0.038) and overall genetic diversity is comparable to previously published estimates throughout the native range of Brook Trout (H O = 0.610; HE = 0.618). Analysis of genetic differentiation among sites indicates that sites in the reclamation area may function as a metapopulation, with fine-scale genetic structure present among tributaries that are connected by gene flow. Understanding how the landscape influences connectivity and population persistence will provide sciencebased guidance for Brook Trout removal efforts and allow managers to release GBCT in stretches of key habitat that ensure the highest probability of reintroduction success.

Colorado↗
USGS2019

State-space analysis of power to detect regional brook trout population trends over time

Threats to aquatic biodiversity are expressed at broad spatial scales, but identifying regional trends in abundance is challenging owing to variable sampling designs, and temporal and spatial variation in abundance. We compiled a regional dataset of brook trout Salvelinus fontinalis counts across their southern range representing 326 sites from eight states between 1982-2014, and conducted a statistical power analysis using Bayesian state-space models to evaluate the ability to detect temporal trends by characterizing posterior distributions with three approaches. A combination of monitoring periods, number of sites and electrofishing passes, decline magnitude and different revisit patterns were tested. Power increased with monitoring periods and decline magnitude. Trends in adults were better detected than young-of-the-year fish, which showed greater inter-annual variation in abundance. The addition of weather covariates to account for the temporal variation increased power only slightly. Single- and three-pass electrofishing methods were similar in power. Finally, power was higher for sampling designs with more frequent revisits over the duration of the monitoring program. Our results provide guidance for broad-scale monitoring designs for temporal trend detection.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2018

Seasonal streamflow extremes are key drivers of Brook Trout young‐of‐the‐year abundance

To manage ecosystems in the context of climate change, we need to understand the relationship between extreme events and population dynamics. Floods and droughts are projected to occur more frequently, but how aquatic species will respond to these extreme events remains uncertain. Based on counts of Brook Trout ( Salvelinus fontinalis ) collected over 28 yr at 115 sites in Shenandoah National Park, we developed mixed‐effects models to (1) assess how well extreme streamflow, as compared to mean flows and total precipitation, can explain young‐of‐the‐year (YOY) abundance, (2) identify potential nonlinear relationships between seasonal environmental covariates and abundance using nonlinear generalized additive mixed models, and (3) explore likely impacts of expected future weather and streamflow conditions. We found that (1) using covariates of streamflow extremes improved prediction of YOY abundance compared to use of mean seasonal flow values or precipitation as a proxy, (2) warmer maximum daily spring temperatures were associated with increased YOY abundance up to about 1.5 standard deviations, above which abundance declined, and (3) a strong negative effect of extreme winter streamflow, unlikely to be offset by possibly positive effects from other seasons, is expected to have a detrimental impact on Brook Trout populations given predicted increases in winter precipitation. Because YOY abundance is a strong determinant of population dynamics for these short‐lived species, extreme events will have the potential to exert a strong influence on population persistence of Brook Trout in a changing climate. Management actions that maximize resiliency of populations in response to extreme events, such as restoration of habitat connectivity, should be prioritized to buffer negative impacts.

Virginia↗
USGS2015

Seasonal temperature and precipitation regulate brook trout young-of-the-year abundance and population dynamics

Abundance of the young‐of‐the‐year (YOY) fish can vary greatly among years and it may be driven by several key biological processes (i.e. adult spawning, egg survival and fry survival) that span several months. However, the relative influence of seasonal weather patterns on YOY abundance is poorly understood. We assessed the importance of seasonal air temperature (a surrogate for stream temperature) and precipitation (a surrogate for stream flow) on brook trout ( Salvelinus fontinalis ) YOY summer abundance using a 29‐year data set from 115 sites in Shenandoah National Park, Virginia, U.S.A. We used a Bayesian hierarchical model that allowed the effect of seasonal weather covariates to vary among sites and accounted for imperfect detection of individuals. Summer YOY abundance was affected by preceding seasonal air temperature and precipitation, and these regional‐scale drivers led to spatial synchrony in YOY abundance dynamics across the 170‐km‐long study area. Mean winter precipitation had the greatest effect on YOY abundance and the relationship was negative. Mean autumn precipitation, and winter and spring temperature had significantly positive effects on YOY abundance, and mean autumn temperature had a significant negative effect. In addition, the effect of summer precipitation differed along a latitudinal gradient, with YOY abundance at more northern sites being more responsive to inter‐annual variation in summer precipitation. Strong YOY years resulted in high abundance of adults (>age 1 + fish) in the subsequent year at more than half of sites. However, higher adult abundance did not result in higher YOY abundance in the subsequent year at any of the study sites (i.e. no positive stock–recruitment relationship). Our results indicate that YOY abundance is a key driver of brook trout population dynamics that is mediated by seasonal weather patterns. A reliable assessment of climate change impacts on brook trout needs to account for how alternations in seasonal weather patterns impact YOY abundance and how such relationships may differ across the range of brook trout distribution.

Virginia↗
USGS2015

Seasonal weather patterns drive population vital rates and persistence in a stream fish

Climate change affects seasonal weather patterns, but little is known about the relative importance of seasonal weather patterns on animal population vital rates. Even when such information exists, data are typically only available from intensive fieldwork (e.g., mark–recapture studies) at a limited spatial extent. Here, we investigated effects of seasonal air temperature and precipitation (fall, winter, and spring) on survival and recruitment of brook trout ( Salvelinus fontinalis ) at a broad spatial scale using a novel stage‐structured population model. The data were a 15‐year record of brook trout abundance from 72 sites distributed across a 170‐km‐long mountain range in Shenandoah National Park, Virginia, USA. Population vital rates responded differently to weather and site‐specific conditions. Specifically, young‐of‐year survival was most strongly affected by spring temperature, adult survival by elevation and per‐capita recruitment by winter precipitation. Low fall precipitation and high winter precipitation, the latter of which is predicted to increase under climate change for the study region, had the strongest negative effects on trout populations. Simulations show that trout abundance could be greatly reduced under constant high winter precipitation, consistent with the expected effects of gravel‐scouring flows on eggs and newly hatched individuals. However, high‐elevation sites would be less vulnerable to local extinction because they supported higher adult survival. Furthermore, the majority of brook trout populations are projected to persist if high winter precipitation occurs only intermittently (≤3 of 5 years) due to density‐dependent recruitment. Variable drivers of vital rates should be commonly found in animal populations characterized by ontogenetic changes in habitat, and such stage‐structured effects may increase population persistence to changing climate by not affecting all life stages simultaneously. Yet, our results also demonstrate that weather patterns during seemingly less consequential seasons (e.g., winter precipitation) can have major impacts on animal population dynamics.

Virginia↗
USGS2014

Spatial variability in survival of adult brook trout within two intensively surveyed headwater stream networks

Headwater stream networks are considered heterogeneous riverscapes, but it is challenging to characterize spatial variability in demographic rates. We estimated site-scale (50 m) survival of adult (>age 1+) brook trout (Salvelinus fontinalis) within two intensively surveyed headwater stream networks by applying an open-population N-mixture approach to count data collected over two consecutive summers. The estimated annual apparent survival rate was 0.37 (95% CI: 0.28–0.46) in one network and 0.31 (95% CI: 0.15–0.45) in the other network. In both networks, trout survival was higher in stream sites characterized by more abundant pool habitats. Trout survival was negatively associated with mean depth in one network and positively associated with stream gradient in the other. Stream temperature was not related to trout survival in either network, possibly because the majority of sites were thermally suitable. A similar analytical approach can be useful for inferring survival rates when count data are available over space and time but individual tagging is not feasible.

Connecticut↗