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Benjamin H. Letcher

Publications and source records attributed to Benjamin H. Letcher.

At least 19 recordsLinked to original sources

Technical note: A low-cost approach to monitoring relative streamflow dynamics in small headwater streams using time lapse imagery and a deep learning model

Despite their ubiquity and importance as freshwater habitat, small headwater streams are under-monitored by existing stream gage networks. To address this gap, we describe a low-cost, non-contact, and low-effort method that enables organizations to monitor relative streamflow dynamics in small headwater streams. The method uses a camera to capture repeat images of the stream from a fixed position. A person then annotates pairs of images, in each case indicating which image has more apparent streamflow or indicating equal flow if no difference is discernible. A deep learning modeling framework called streamflow rank estimation (SRE) is then trained on the annotated image pairs and applied to rank all images from highest to lowest apparent streamflow. From this result a relative hydrograph can be derived. We found that our modeled relative hydrograph dynamics matched the observed hydrograph dynamics well for 11 cameras at 8 streamflow sites in western Massachusetts. Higher performance was observed during the annotation period (median Kendall's Tau rank correlation of 0.75, with a range of 0.6–0.83) than after it (median Kendall's Tau of 0.59, with range 0.34–0.74). We found that annotation performance was generally consistent across the 11 camera sites and 2 individual annotators and was positively correlated with streamflow variability at a site. A scaling simulation determined that model performance improvements were limited after 1000 annotation pairs. Our model's estimates of relative flow, while not equivalent to absolute flow, may still be useful for many applications, such as ecological modeling and calculating event-based hydrological statistics (e.g., the number of out-of-bank floods). We anticipate that this method will be a valuable tool to extend existing stream monitoring networks and provide new insights on dynamic headwater systems.

Massachusetts

Negative growth in body mass of trout and salmon in a small stream network

In species inhabiting stressful environments, some individuals experience negative growth in body mass during their lives, potentially influencing survival, reproduction, populations, and ecosystems. Using data from a long-term (1997–2015) study of brook trout ( Salvelinus fontinalis ), brown trout ( Salmo trutta ), and juvenile Atlantic salmon ( Salmo salar ) in Massachusetts, USA, we analyzed the frequency, causes, and consequences of seasonal mass loss. Negative growth occurred in 14.8% of observations (3573 instances), with the highest prevalence during summer (June–September). Species differed markedly: 42.5% of juvenile Atlantic salmon, 24.9% of brook trout, but only 7.7% of brown trout exhibited negative growth. The likelihood of mass loss increased with size, age, and low stream flows, particularly in summer. Brook trout in the small or isolated tributaries exhibited less summer mass loss than those in the larger streams. Other factors, including temperature and population density, had minimal or inconsistent effects. Individuals experiencing negative growth, especially brook trout in summer and autumn, were less likely to be re-encountered. As we observed no association of mass loss with movement, this suggests a potential survival cost of negative body mass growth.

Massachusetts

How repeatable is CTmax within individual brook trout over short- and long-time intervals?

As stream temperatures increase due to factors such as heated runoff from impervious surfaces, deforestation, and climate change, fish species adapted to cold water streams are forced to move to more suitable habitat, acclimate or adapt to increased thermal regimes, or die. To estimate the potential for adaptation, a (within individual) repeatable metric of thermal tolerance is imperative. Critical thermal maximum (CTmax) is a dynamic test that is widely used to measure thermal tolerance across many taxa and has been used in fishes for decades, but its repeatability in most species is unknown. CTmax tests increase water temperature steadily over time until loss of equilibrium (LOE) is achieved. To determine if CTmax is a consistent metric within individual fish, we measured CTmax on the same lab-held individually-marked adult brook trout Salvelinus fontinalis at three different times (August & September 2016, September 2017). We found that CTmax is a repeatable trait (Repeatability ± S.E.: 0.48 ± 0.14). CTmax of individuals males was consistent over time, but the CTmax of females increased slightly over time. This result indicates that CTmax is a robust, repeatable estimate of thermal tolerance in a cold-water adapted fish.

Journal of Thermal Biology

Survival and density of a dominant fish species across a gradient of urbanization in North Carolina tidal creeks

Development in the southeastern U.S. coastal plain generates the need for a better understanding of how demographics (survival and abundance) of estuarine nekton respond to urbanization. Apparent survival and density of the dominant Atlantic coast salt marsh fish, Fundulus heteroclitus, were estimated in four North Carolina tidal creeks using a model simultaneously fitted to mark-resight and mark-recapture data. Rates of weekly loss (mortality plus emigration) were high (~10%). Sampling for tagged fish within- and outside of study creeks showed high site fidelity to each creek, suggesting that loss largely result from mortality rather than emigration. Estimated rates of apparent survival were lowest in the creek with the least instream- and watershed-level impacts relative to creeks with greater impacts; this was also the creek with direct (non-culvert) access downstream to a larger waterbody, suggesting that enhanced access by predators and/or greater rates of permanent emigration may have contributed to loss there. There was a positive relationship between minnow trap catch-per-unit-effort (CPUE) and density; CPUE was used to index density so that the relationship between it and habitat and urbanization effects could be examined in two additional (six total) study creeks. Highest CPUE estimates occurred early in each growing season and were associated with creeks possessing characteristics most representative of undisturbed salt marsh mosaics: high percentages of marsh coverage instream and downstream and greatest percentages of marsh edge. Given generally limited movement outside of creeks, differences in abundance among creeks likely result from different levels of recruitment that are related to salt marsh availability. Natural resource planners should prioritize preservation of salt marsh habitats to maintain abundance levels of this trophically important species.

North Carolina

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

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

A geostatistical state‐space model of animal densities for stream networks

Population dynamics are often correlated in space and time due to correlations in environmental drivers as well as synchrony induced by individual dispersal. Many statistical analyses of populations ignore potential autocorrelations and assume that survey methods (distance and time between samples) eliminate these correlations, allowing samples to be treated independently. If these assumptions are incorrect, results and therefore inference may be biased and uncertainty underestimated. We developed a novel statistical method to account for spatiotemporal correlations within dendritic stream networks, while accounting for imperfect detection in the surveys. Through simulations, we found this model decreased predictive error relative to standard statistical methods when data were spatially correlated based on stream distance and performed similarly when data were not correlated. We found that increasing the number of years surveyed substantially improved the model accuracy when estimating spatial and temporal correlation coefficients, especially from 10 to 15 yr. Increasing the number of survey sites within the network improved the performance of the nonspatial model but only marginally improved the density estimates in the spatiotemporal model. We applied this model to brook trout data from the West Susquehanna Watershed in Pennsylvania collected over 34 yr from 1981 to 2014. We found the model including temporal and spatiotemporal autocorrelation best described young of the year (YOY) and adult density patterns. YOY densities were positively related to forest cover and negatively related to spring temperatures with low temporal autocorrelation and moderately high spatiotemporal correlation. Adult densities were less strongly affected by climatic conditions and less temporally variable than YOY but with similar spatiotemporal correlation and higher temporal autocorrelation.

Ecological Applications

Three visualization approaches for communicating and exploring PIT tag data

As the number, size and complexity of ecological datasets has increased, narrative and interactive raw data visualizations have emerged as important tools for exploring and understanding these large datasets. As a demonstration, we developed three visualizations to communicate and explore passive integrated transponder tag data from two long-term field studies. We created three independent visualizations for the same dataset, allowing separate entry points for users with different goals and experience levels. The first visualization uses a narrative approach to introduce users to the study. The second visualization provides interactive cross-filters that allow users to explore multi-variate relationships in the dataset. The last visualization allows users to visualize the movement histories of individual fish within the stream network. This suite of visualization tools allows a progressive discovery of more detailed information and should make the data accessible to users with a wide variety of backgrounds and interests.

Maine, Massachusetts

Experimental test of genetic rescue in isolated populations of brook trout

Genetic rescue is an increasingly considered conservation measure to address genetic erosion associated with habitat loss and fragmentation. The resulting gene flow from facilitating migration may improve fitness and adaptive potential, but is not without risks (e.g., outbreeding depression). Here, we conducted a test of genetic rescue by translocating ten (five of each sex) brook trout ( Salvelinus fontinalis ) from a single source to four nearby and isolated stream populations. To control for the demographic contribution of translocated individuals, ten resident individuals (five of each sex) were removed from each recipient population. Prior to the introduction of translocated individuals, the two smallest above-barrier populations had substantially lower genetic diversity, and all populations had reduced effective number of breeders relative to adjacent below-barrier populations. In the first reproductive bout following translocation, 31 of 40 (78%) translocated individuals reproduced successfully. Translocated individuals contributed to more families than expected under random mating and generally produced larger full-sibling families. We observed relatively high (>20%) introgression in three of the four recipient populations. The translocations increased genetic diversity of recipient populations by 45% in allelic richness and 25% in expected heterozygosity. Additionally, strong evidence of hybrid vigour was observed through significantly larger body sizes of hybrid offspring relative to resident offspring in all recipient populations. Continued monitoring of these populations will test for negative fitness effects beyond the first generation. However, these results provide much-needed experimental data to inform the potential effectiveness of genetic rescue-motivated translocations.

Virginia

Estimating thermal performance curves from repeated field observations

Estimating thermal performance of organisms is critical for understanding population distributions and dynamics and predicting responses to climate change. Typically, performance curves are estimated using laboratory studies to isolate temperature effects, but other abiotic and biotic factors influence temperature-performance relationships in nature reducing these models' predictive ability. We present a model for estimating thermal performance curves from repeated field observations that includes environmental and individual variation. We fit the model in a Bayesian framework using MCMC sampling, which allowed for estimation of unobserved latent growth while propagating uncertainty. Fitting the model to simulated data varying in sampling design and parameter values demonstrated that the parameter estimates were accurate, precise, and unbiased. Fitting the model to individual growth data from wild trout revealed high out-of-sample predictive ability relative to laboratory-derived models, which produced more biased predictions for field performance. The field-based estimates of thermal maxima were lower than those based on laboratory studies. Under warming temperature scenarios, field-derived performance models predicted stronger declines in body size than laboratory-derived models, suggesting that laboratory-based models may underestimate climate change effects. The presented model estimates true, realized field performance, avoiding assumptions required for applying laboratory-based models to field performance, which should improve estimates of performance under climate change and advance thermal ecology.

Ecology

Implanting 8-mm passive integrated transponder tags into small Brook Trout: Effects on growth and survival in the laboratory

Passive integrated transponder (PIT) tags are commonly used to investigate relationships between individual fish and their environment. The recent availability of smaller tags has provided the opportunity to tag smaller fish. In this study, we implanted 8-mm PIT tags into small Brook Trout Salvelinus fontinalis (35–50 mm FL; 0.35–1.266 g) and compared tag retention, growth rates, and survival of PIT-tagged fish with those of fish subjected to handling only or to handling plus fin clipping. We also examined how initial size at tagging affected absolute and specific growth rates of PIT-tagged individuals over time. We found that survival was 100%, tag retention was 96.7%, and fish size did not vary across treatments at 29 and 64 d posttagging. Additionally, there was no evidence that growth rate (FL or mass) was influenced by the initial size of the fish that were PIT tagged. Our results indicate that retention rates of 8-mm PIT tags surgically implanted into small Brook Trout are high and that there is no discernible effect on growth or survival in the laboratory. The ability to implant smaller PIT tags into smaller fish earlier in the season would allow researchers conducting PIT tag studies to expand demographic models to estimate survival of age-0 fish through the summer of their first year.

North American Journal of Fisheries Management

A hierarchical model of daily stream temperature using air-water temperature synchronization, autocorrelation, and time lags

Water temperature is a primary driver of stream ecosystems and commonly forms the basis of stream classifications. Robust models of stream temperature are critical as the climate changes, but estimating daily stream temperature poses several important challenges. We developed a statistical model that accounts for many challenges that can make stream temperature estimation difficult. Our model identifies the yearly period when air and water temperature are synchronized, accommodates hysteresis, incorporates time lags, deals with missing data and autocorrelation and can include external drivers. In a small stream network, the model performed well (RMSE = 0.59°C), identified a clear warming trend (0.63 °C decade −1 ) and a widening of the synchronized period (29 d decade −1 ). We also carefully evaluated how missing data influenced predictions. Missing data within a year had a small effect on performance (∼0.05% average drop in RMSE with 10% fewer days with data). Missing all data for a year decreased performance (∼0.6 °C jump in RMSE), but this decrease was moderated when data were available from other streams in the network.

PeerJ

Changes in seasonal climate outpace compensatory density-dependence in eastern brook trout

Understanding how multiple extrinsic (density-independent) factors and intrinsic (density-dependent) mechanisms influence population dynamics has become increasingly urgent in the face of rapidly changing climates. It is particularly unclear how multiple extrinsic factors with contrasting effects among seasons are related to declines in population numbers and changes in mean body size and whether there is a strong role for density-dependence. The primary goal of this study was to identify the roles of seasonal variation in climate driven environmental direct effects (mean stream flow and temperature) versus density-dependence on population size and mean body size in eastern brook trout (Salvelinus fontinalis). We use data from a 10-year capture-mark-recapture study of eastern brook trout in four streams in Western Massachusetts, USA to parameterize a discrete-time population projection model. The model integrates matrix modeling techniques used to characterize discrete population structures (age, habitat type and season) with integral projection models (IPMs) that characterize demographic rates as continuous functions of organismal traits (in this case body size). Using both stochastic and deterministic analyses we show that decreases in population size are due to changes in stream flow and temperature and that these changes are larger than what can be compensated for through density-dependent responses. We also show that the declines are due mostly to increasing mean stream temperatures decreasing the survival of the youngest age class. In contrast, increases in mean body size over the same period are the result of indirect changes in density with a lesser direct role of climate-driven environmental change.

Massachusetts

Movement patterns of Brook Trout in a restored coastal stream system in southern Massachusetts

Coastal Brook Trout ( Salvelinus fontinalis ) populations are found from northern Canada to New England. The extent of anadromy generally decreases with latitude, but the ecology and movements of more southern populations are poorly understood. We conducted a 33-month acoustic telemetry study of Brook Trout in Red Brook, MA, and adjacent Buttermilk Bay (marine system) using 16 fixed acoustic receivers and surgically implanting acoustic transmitters in 84 individuals. Tagged Brook Trout used the stream, estuary (50% of individuals) and bay (10% of individuals). Movements into full sea water were brief when occurring. GAMM models revealed that transitions between habitat areas occurred most often in spring and fall. Environmental data suggest that use of the saline environment is limited by summer temperatures in the bay. Movements may also be related to moon phase. Compared to more northern coastal populations of Brook Trout, the Red Brook population appears to be less anadromous overall, yet the estuarine segment of the system may have considerable ecological importance as a food resource.

Ecology of Freshwater Fish

Modeling structured population dynamics using data from unmarked individuals

The study of population dynamics requires unbiased, precise estimates of abundance and vital rates that account for the demographic structure inherent in all wildlife and plant populations. Traditionally, these estimates have only been available through approaches that rely on intensive mark–recapture data. We extended recently developed N -mixture models to demonstrate how demographic parameters and abundance can be estimated for structured populations using only stage-structured count data. Our modeling framework can be used to make reliable inferences on abundance as well as recruitment, immigration, stage-specific survival, and detection rates during sampling. We present a range of simulations to illustrate the data requirements, including the number of years and locations necessary for accurate and precise parameter estimates. We apply our modeling framework to a population of northern dusky salamanders ( Desmognathus fuscus ) in the mid-Atlantic region (USA) and find that the population is unexpectedly declining. Our approach represents a valuable advance in the estimation of population dynamics using multistate data from unmarked individuals and should additionally be useful in the development of integrated models that combine data from intensive (e.g., mark–recapture) and extensive (e.g., counts) data sources.

Ecology

Estimating movement and survival rates of a small saltwater fish using autonomous antenna receiver arrays and passive integrated transponder tags

We evaluated the performance of small (12.5 mm long) passive integrated transponder (PIT) tags and custom detection antennas for obtaining fine-scale movement and demographic data of mummichog Fundulus heteroclitus in a salt marsh creek. Apparent survival and detection probability were estimated using a Cormack Jolly Seber (CJS) model fitted to detection data collected by an array of 3 vertical antennas from November 2010 to March 2011 and by a single horizontal antenna from April to August 2011. Movement of mummichogs was monitored during the period when the array of vertical antennas was used. Antenna performance was examined in situ using tags placed in wooden dowels (drones) and in live mummichogs. Of the 44 tagged fish, 42 were resighted over the 9 mo monitoring period. The in situ detection probabilities of the drone and live mummichogs were high (~80-100%) when the ambient water depth was less than ~0.8 m. Upstream and downstream movement of mummichogs was related to hourly water depth and direction of tidal current in a way that maximized time periods over which mummichogs utilized the intertidal vegetated marsh. Apparent survival was lower during periods of colder water temperatures in December 2010 and early January 2011 (median estimate of daily apparent survival = 0.979) than during other periods of the study (median estimate of daily apparent survival = 0.992). During late fall and winter, temperature had a positive effect on the CJS detection probability of a tagged mummichog, likely due to greater fish activity over warmer periods. During the spring and summer, this pattern reversed possibly due to mummichogs having reduced activity during the hottest periods. This study demonstrates the utility of PIT tags and continuously operating autonomous detection systems for tracking fish at fine temporal scales, and improving estimates of demographic parameters in salt marsh creeks that are difficult or impractical to sample with active fishing gear.

Marine Ecology Progress Series

Basin-scale phenology and effects of climate variability on global timing of initial seaward migration of Atlantic salmon (Salmo salar)

Migrations between different habitats are key events in the lives of many organisms. Such movements involve annually recurring travel over long distances usually triggered by seasonal changes in the environment. Often, the migration is associated with travel to or from reproduction areas to regions of growth. Young anadromous Atlantic salmon ( Salmo salar ) emigrate from freshwater nursery areas during spring and early summer to feed and grow in the North Atlantic Ocean. The transition from the freshwater (‘parr’) stage to the migratory stage where they descend streams and enter salt water (‘smolt’) is characterized by morphological, physiological and behavioural changes where the timing of this parr-smolt transition is cued by photoperiod and water temperature. Environmental conditions in the freshwater habitat control the downstream migration and contribute to within- and among-river variation in migratory timing. Moreover, the timing of the freshwater emigration has likely evolved to meet environmental conditions in the ocean as these affect growth and survival of the post-smolts. Using generalized additive mixed-effects modelling, we analysed spatio-temporal variations in the dates of downstream smolt migration in 67 rivers throughout the North Atlantic during the last five decades and found that migrations were earlier in populations in the east than the west. After accounting for this spatial effect, the initiation of the downstream migration among rivers was positively associated with freshwater temperatures, up to about 10 °C and levelling off at higher values, and with sea-surface temperatures. Earlier migration occurred when river discharge levels were low but increasing. On average, the initiation of the smolt seaward migration has occurred 2.5 days earlier per decade throughout the basin of the North Atlantic. This shift in phenology matches changes in air, river, and ocean temperatures, suggesting that Atlantic salmon emigration is responding to the current global climate changes.

Global Change Biology