Geology topics

Daniel S. Stich

Publications and source records attributed to Daniel S. Stich.

15 recordsLinked to original sources

USGS2026

Longitudinal variability of demographics and life history in an anadromous spawning population within a large, unimpeded East Coast, USA, watershed

Objective The goal of this study was to characterize the variability in age, growth, and life history of sea-run fish throughout a large, East Coast, USA, watershed to improve the parameterization of longitudinal variation in demographics and spawning histories in an undammed river. Methods Both live and dead American Shad Alosa sapidissima were collected during spring 2020 and 2021. Sex, length, age, and repeat spawning information were recorded for all individuals ( n = 512). Growth curves were created to test hypotheses about the variables that were related to the growth rates of American Shad for this relatively unsampled portion of the spawning population in the Delaware River. Results We observed variation in size, age, repeat spawning probability and propensity, and sex ratios from downstream to upstream as well as during the spawning season. Individual traits also varied among the fish that died during migration and those that were collected alive. Conclusions This study expands the current knowledge about variability in the life history traits that are commonly used in assessing and managing an anadromous fish that spawns upstream in a large, undammed watershed. Our results have broad implications for the assessment and management of anadromous fish populations globally and contribute to understanding parity along a continuum. Some potential priorities for future work include using telemetry to understand the final disposition of live fish, investigating fine-scale genetic control for correlated life-history traits, and investigating the correlations between natal origin (i.e., genetic stock mixing) and longitudinal variation within spawning populations.

New York, Pennsylvania↗

USGS2025

Reconstructing relative abundance indices for Atlantic sturgeon using hierarchical ecological models

Objective The Atlantic Sturgeon Acipenser oxyrinchus is a wide-ranging, long-lived diadromous fish that is endangered in most of its range. Our objective was to develop and apply long-term, detection-corrected indices of relative abundance for juvenile and adult Atlantic Sturgeon in the Hudson River, New York, United States, to support population monitoring and stock assessment. Methods We used long-term gill-net catches to estimate relative abundances of juvenile and adult Atlantic Sturgeon while accounting for imperfect detection within an N- mixture modeling framework. We validated the model framework using a simulation–estimation framework based on mean parameter estimates from the adult Atlantic Sturgeon relative abundance index. Results Simulation testing indicated that absolute abundance estimates may be biased low due to poor characterization of detection probabilities. However, model estimates of relative abundance tracked simulated abundance trends well. Juvenile relative abundance estimates followed similar trends as raw gill-net catches but were less variable among years when corrected for detection probability. Relative abundance of juveniles increased from 2004 to 2015 prior to declining through 2022, with little evidence for change between the start and end of the survey. Detection-corrected indices for adult sturgeon indicated a consistent increase in relative abundance that was not readily apparent in raw catch indices. Conclusions Detection-corrected catch indices can provide improved characterization of Atlantic Sturgeon relative abundance dynamics over raw gill-net catches through use of N- mixture models. The approach has broad applicability to data types that are commonly collected for understanding population trends in stock assessment. Estimation of absolute abundance and other population demographics germane to management would benefit from alternative or auxiliary data collected through approaches such as side-scan sonar or acoustic telemetry, which are increasingly common for monitoring sturgeon populations.

New York↗

USGS2025

anadrofish: Anadromous fish population responses to dams

Diadromous fishes world-wide experienced precipitous declines during the 19th and 20th centuries due to a combination of overfishing, pollution, and freshwater habitat loss through construction of dams (Limburg & Waldman, 2009). Following wide-spread fishing closures and large-scale remediation of many historical pollution sources, dams in coastal rivers remain as the largest tractable impediment to population recovery for many of these species (Waldman & Quinn, 2022). In some cases, dams reduce access to as much as 95% of freshwater and rearing habitat (Hall et al., 2011). These effects are especially pronounced for species that rely on long-distance migrations to spawning and rearing habitat upstream of barriers such as various alosines (herrings; e.g., American shad Alosa sapidissima , alewife A. pseudoharengus , and blueback herring A. aestivalis (Noonan et al., 2012)) and salmonines (trout and salmon; e.g., Salmo spp. (Parrish et al., 1998) and Oncorhynchus spp. (Quiñones et al., 2015). Traditional stock assessment tools such as per-recruit analyses often fail to capture management complexities related to diadromous life histories such as fish passage at dams, and integrated assessment models can be difficult to parameterize for data-poor species such as herrings (Atlantic States Marine Fisheries Commission, 2024). This has resulted in the development of species- and system-specific approaches to fisheries stock assessment and management strategy evaluation (Barber et al., 2018; Nieland et al., 2015; Roy et al., 2018; Stich et al., 2019). We created the anadrofish package (Stich, Hardesty, et al., 2025) for R (R Core Team, 2025) to provide a generalized approach that also allows broader application to novel species, systems, and scenarios.

Journal of Open Source Software↗

USGS2023

Seven dam challenges for migratory fish: Insights from the Penobscot River

More than a century of impoundments in the Penobscot River, Maine, USA, has contributed to population declines in migratory fish in the system. A decade of change, research, and monitoring has revealed direct and indirect ways that dams have influenced the river habitat, connectivity for migratory fish, and the food web. The removal of two main-stem dams (in 2012 and 2013) and bolstering of fish passage have been part of coordinated restoration efforts in the watershed. Integral to this undertaking was support for short- and long-term monitoring and research that included physical habitat, fish passage, and broad scale ecological assessments. Herein we discuss the seven interconnected and complex ways that dams have affected the Penobscot River ecosystem, particularly for migratory fish. These include familiar influences ascribed to dams: i) impaired access to habitat, ii) injury and mortality, and iii) delays of migration. Other ecological influences are less studied and more subtle: iv) facilitation of predation, v) community shifts, and vi) demographic shifts. Lastly, dams result in vii) a loss of ecosystem services that would otherwise be intact in an unimpounded system. We draw on both direct examples from the Penobscot River and broader information to characterize how impoundments have transformed this ecosystem for more than a century. Recent dam removals and mitigation efforts have reestablished some of these ecological functions.

Maine↗

USGS2023

Use of environmental DNA to assess American Eel distribution, abundance, and barriers in a river-canal system

Objective: The American Eel Anguilla rostrata historically was one of the most common fish species in Atlantic coast watersheds, but extensive dam construction and other factors caused a widespread population decline. One of the watersheds where American Eels have declined considerably is the Mohawk River in eastern and central New York. Recent attempts to characterize the distribution and abundance of American Eels in this watershed have been ineffective, and the extent to which a series of locks and dams on the Hudson River and lower Mohawk River limits use of the watershed is unclear. Methods: We developed a model between environmental DNA (eDNA) quantity and American Eel abundance in the Hudson River watershed in which the DNA concentration in water samples explained up to 65% of the variability in eel density and 56% of the variability in eel biomass. We then used this relationship to interpret eDNA data collected twice from 36 sites across the Mohawk River watershed in 2021 and make inferences about the distribution and abundance of American Eels. Result: American Eel DNA was detected almost exclusively in the downstream-most 4 km of the Mohawk River within a series of barriers. The concentration of DNA was reduced by approximately 80% across each successive upstream barrier before becoming too low to detect consistently. Our data suggest that eel population density was high in the Hudson River estuary and declined rapidly in the lower Mohawk River, and the species was nearly absent or undetectable in the Mohawk River and its tributaries upstream of the Crescent Dam and the Waterford Flight of Locks. Conclusion: Barriers appear to be largely restricting American Eels from using over 99% of the Mohawk River watershed. Therefore, improvements in fish passage at dams and hydroelectric facilities in the region could help the American Eel to regain access to this part of its native range.

New York↗

USGS2022

Effects of dam-induced delays on system-wide survival of Atlantic salmon smolts during high-flow, high-survival years in the Penobscot River, Maine, USA

System-wide survival of hatchery-reared Atlantic salmon ( Salmo salar ) smolts was evaluated (2017–2019) in the Penobscot River and compared to survival estimates from previous years that spanned major changes (2005–2016). This system was transformed through two dam removals in 2012 and construction of a nature-like passage structure at a third. The main stem had three dams (five prior to 2012), while the main tributary had four dams (one with the new nature-like passage). We estimated survival using acoustic telemetry mark–recapture ( n = 1482) from 2017 to 2019. Six release sites and two release dates were included to assess system-wide survival. Survival from 2017 to 2019 was higher than previous years, with total cumulative survival > 0.75, independently of year and release sites, compared to survival < 0.5 in previous years. These years coincided with exceptional high flows not seen previously. We found an effect of delays on survival, longer delays associated with lower survival. Overall, survival in these years increased in all reaches relative to previous years except for one dam, Weldon Dam, which was a site of sustained high mortality.

Maine↗

USGS2022

FishStan: Hierarchical Bayesian models for fisheries

Fisheries managers and ecologists use statistical models to estimate population-level relations and demographic rates (e.g., length-maturity curves, growth curves, and mortality rates). These relations and rates provide insight into populations and inputs for other models. For example, growth curves may vary across lakes showing fish populations differ due to management actions or underlying environmental conditions. A fisheries manager could use this information to set lake-specific harvest limits or an ecologist could use this information to test scientific hypotheses about fish populations. The above example also demonstrates how populations exist within hierarchical structures where sub-populations may be nested within a meta-population. More generally, these hierarchical structures may be both biological (e.g., different lakes or river pools) and statistical (e.g., correlated error structures). Currently, limited options exist for fitting these hierarchical models and people seeking to use them often must program their own implementations. Furthermore, many fisheries managers and researchers may not have Bayesian programming skills, but many can use interactive languages such as R. Additionally, programs such as JAGS often require long run times (e.g., hours if not days) to fit hierarchical models and programs such as Stan can be more difficult to program because it is a compiled language. We created fishStan to share hierarchical models for fisheries and ecology in an easy-to-use R package.

Journal of Open Source Software↗

USGS2021

What have we lost? Modeling dam impacts on American shad populations through their native range

American shad ( Alosa sapidissima ) are native to the east coast of North America from the St. Johns River, Florida, to the St. Lawrence River region in Canada. Since the 1800s, dams have reduced access to spawning habitat. To assess the impact of dams, we estimated the historically accessed spawning habitat in coastal rivers (485,618 river segments with 21,113 current dams) based on (i) width, (ii) distance from seawater, and (iii) slope (to exclude natural barriers to migration) combined with local knowledge. Estimated habitat available prior to dam construction (2,752 km 2 ) was 41% greater than current fully accessible habitat (1,639 km 2 ). River-specific population models were developed using habitat estimates and latitudinally appropriate life history parameters (e.g., size at age, maturity, iteroparity). Estimated coast-wide annual production potential was 69.1 million spawners compared with a dammed scenario (41.8 million spawners). Even with optimistic fish passage performance assumed for all dams (even if passage is completely absent), the dam-imposed deficit was alleviated by fewer than 3 million spawners. We estimate that in rivers modeled without dams, 98,000 metric tons of marine sourced biomass and nutrients were annually delivered, 60% of which was retained through carcasses, gametes and metabolic waste. Damming is estimated to have reduced this by more than one third. Based on our results, dams represent a significant and acute constraint to the population and, with other human impacts, reduce the fishery potential and ecological services attributed to the species.

Frontiers in Marine Science↗

USGS2021

Climate change may cause shifts in growth and instantaneous natural mortality of American Shad throughout their native range

American Shad Alosa sapidissima is an anadromous species with populations ranging along the U.S. Atlantic coast. Past American Shad stock assessments have been data limited and estimating system-specific growth parameters or instantaneous natural mortality ( M ) was not possible. This precluded system-specific stock assessment and management due to reliance on these parameters for estimating other population dynamics (such as yield per recruit). Furthermore, climate-informed biological reference points remain a largely unaddressed need in American Shad stock assessment. Population abundance estimates of American Shad and other species often rely heavily on M derived from von Bertalanffy growth function (VBGF) parameters. Therefore, we developed Bayesian hierarchical models to estimate coastwide, regional, and system-specific VBGF parameters and M using data collected from 1982 to 2017. We tested predictive performance of models that included effects of various climate variables on VBGF parameters within these models. System-specific models were better supported than regional or coast-wide models. Mean asymptotic length ( L ∞ ) decreased with increasing mean annual sea surface temperature (SST) and degree days (DD) experienced by fish during their lifetime. Although uncertain, K (Brody growth coefficient) decreased over the same range of lifetime SST and DD. Assuming no adaptation, we projected changes in VBGF parameters and M through 2099 using modeled SST from two climate projection scenarios (Representative Concentration Pathways 4.5 and 8.5). We predicted reduced growth under both scenarios, and M was projected to increase by about 0.10. It is unclear how reduced growth and increased mortality may influence population productivity or life history adaptation in the future, but our results may inform stock assessment models to assess those trade-offs.

Transactions of the American Fisheries Society↗

USGS2019

Temporal variability in stream fish assemblage metrics and implications for long-term monitoring

High natural variability in the condition of fish communities in headwater streams complicates detection of long-term responses to changes in water quality. As a result, little is known about the impacts and recovery of fishes from acid deposition in streams of New York. Twenty-one fish metrics from annual electrofishing surveys at 13 streams sites in the Catskill and Adirondack mountains were assessed to quantify temporal variability and identify effective monitoring strategies for detecting change in headwater stream fish assemblages. Metrics included the density and biomass of Brook Trout populations and entire fish communities using length-, area-, and effort-based standardization techniques. Linear mixed models were used to estimate changes in coefficients of variation (CV) for different classes of metrics and standardization techniques, and a simulation-based power analysis was conducted to assess differences in statistical power for each metric with various sampling designs. Metric CV varied significantly as a result of standardization technique and whether metrics were calculated for the entire community or Brook Trout only. The sampling effort necessary to detect a 30% change with power of 0.80 was strongly correlated with CV (R 2 = 0.77). The number of sampling events at the 13 sites needed to detect this change ranged from 1 to >60, suggesting metric selection can strongly affect statistical power and the resources necessary to detect change. Thus, metric selection is a complex decision that must consider study objectives and biological relevance, in addition to natural variability and statistical power. However, adequate statistical power was achieved at relatively small sample sizes using certain metrics, indicating that fish communities in headwater streams can be a valuable component of long-term assessments of acidification impacts and recovery.

New York↗

USGS2019

Role of recovering river herring population on smallmouth bass diet and growth

Fish assemblages in Atlantic coastal rivers have undergone extensive ecological change in the last two and a half centuries due to human influence, including extirpation of many migratory fish species, such as river herring (Alosa spp.) and introduction of nonnative piscivores, notably Smallmouth Bass Micropterus dolomieu. Recently, dam removals and fish passage improvements in the Penobscot River, Maine, have allowed river herring to return to reaches of the river that have been inaccessible since the late 19th century. Alosine populations have increased and this trend is anticipated to continue. This may increase forage in the system which could potentially increase growth for Smallmouth Bass, the dominant piscivore. We examined the diet and growth of Smallmouth Bass collected from areas of the Penobscot River watershed with and without access to river herring as prey. We collected 765 Smallmouth Bass throughout 2015, examined the stomach contents of 573 individuals, and found notable differences in diet among three river reaches with common seasonal trends. Juvenile river herring composed an average of 19% (SE = ±6%) of stomach contents by mass from Smallmouth Bass collected in the freshwater tidal area but were rarely observed in the diets upstream. We used estimates from von Bertalanffy growth models to examine differences in growth among reaches and found that asymptotic length was the longest (425 mm TL) in the Tidal reach where access to river herring was unrestricted. We then used these data to predict changes to growth associated with increased access to juvenile river herring prey with bioenergetics models. Results indicated that substituting juvenile river herring for less energy-dense prey (e.g.,invertebrates) may lead to increases in seasonal growth throughout the watershed as river herring populations continue to rebound in response to dam removal. Our results provide insight into the diet and growth of Smallmouth Bass in a large New England river, and provide a foundation for future work investigating unfolding changes to these characteristics following recent dam removals.

Maine↗

USGS2017

Hard choices in assessing survival past dams — a comparison of single- and paired-release strategies

Mark–recapture models are widely used to estimate survival of salmon smolts migrating past dams. Paired releases have been used to improve estimate accuracy by removing components of mortality not attributable to the dam. This method is accompanied by reduced precision because ( i ) sample size is reduced relative to a single, large release; and ( ii ) variance calculations inflate error. We modeled an idealized system with a single dam to assess trade-offs between accuracy and precision and compared methods using root mean squared error (RMSE). Simulations were run under predefined conditions (dam mortality, background mortality, detection probability, and sample size) to determine scenarios when the paired release was preferable to a single release. We demonstrate that a paired-release design provides a theoretical advantage over a single-release design only at large sample sizes and high probabilities of detection. At release numbers typical of many survival studies, paired release can result in overestimation of dam survival. Failures to meet model assumptions of a paired release may result in further overestimation of dam-related survival. Under most conditions, a single-release strategy was preferable.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2015

Linking behavior, physiology, and survival of Atlantic Salmon smolts during estuary migration

Decreased marine survival is identified as a component driver of continued declines of Atlantic Salmon Salmo salar . However, estimates of marine mortality often incorporate loss incurred during estuary migration that may be mechanistically distinct from factors affecting marine mortality. We examined movements and survival of 941 smolts (141 wild and 800 hatchery-reared fish) released in freshwater during passage through the Penobscot River estuary, Maine, from 2005 to 2013. We related trends in estuary arrival date, movement rate, and survival to fish characteristics, migratory history, and environmental conditions in the estuary. Fish that experienced the warmest thermal history arrived in the estuary 8 d earlier than those experiencing the coolest thermal history during development. Estuary arrival date was 10 d later for fish experiencing high flow than for fish experiencing low flow. Fish released furthest upstream arrived in the estuary 3 d later than those stocked further downstream but moved 0.5 km/h faster through the estuary. Temporally, movement rate and survival in the estuary both peaked in mid-May. Spatially, movement rate and survival both decreased from freshwater to the ocean. Wild smolts arrived in the estuary later than hatchery fish, but we observed no change in movement rate or survival attributable to rearing history. Fish with the highest gill Na + , K + -ATPase activity incurred 25% lower mortality through the estuary than fish with the lowest gill Na + , K + -ATPase activity. Smolt survival decreased (by up to 40%) with the increasing number of dams passed (ranging from two to nine) during freshwater migration. These results underscore the importance of physiological preparedness on performance and the delayed, indirect effects of dams on survival of Atlantic Salmon smolts during estuary migration, ultimately affecting marine survival estimates.

Marine and Coastal Fisheries: Dynamics, Management↗

USGS2015

Initiation of migration and movement rates of Atlantic salmon smolts in fresh water

Timing of ocean entry is critical for marine survival of both hatchery and wild Atlantic salmon ( Salmo salar ) smolts. Management practices and barriers to migration such as dams may constrain timing of smolt migrations resulting in suboptimal performance at saltwater entry. We modeled influences of stocking location, smolt development, and environmental conditions on ( i ) initiation of migration by hatchery-reared smolts and ( ii ) movement rate of hatchery- and wild-reared Atlantic salmon smolts in the Penobscot River, Maine, USA, from 2005 through 2014 using acoustic telemetry data. We also compared movement rates in free-flowing reaches with rates in reaches with hydropower dams and head ponds. We compared movement rates before and after (1) removal of two mainstem dams and (2) construction of new powerhouses. Initiation of movement by hatchery fish was influenced by smolt development, stocking location, and environmental conditions. Smolts with the greatest gill Na + , K + -ATPase (NKA) activity initiated migration 24 h sooner than fish with the lowest gill NKA activity. Fish with the greatest cumulative thermal experience initiated migration 5 days earlier than those with lowest cumulative thermal experience. Smolts released furthest from the ocean initiated migration earlier than those released downstream, but movement rate increased by fivefold closer to the ocean, indicating behavioral trade-offs between initiation and movement rate. Dams had a strong effect on movement rate. Movement rate increased from 2.8 to 5.4 km·h −1 in reaches where dams were removed, but decreased from 2.1 to 0.1 km·h −1 in reaches where new powerhouses were constructed. Movement rate varied throughout the migratory period and was inversely related to temperature. Fish moved slower at extreme high or low discharge. Responses in fish movement rates to dam removal indicate the potential scope of recovery for these activities.

Maine↗

USGS2014

Photoperiod control of downstream movements of Atlantic salmon Salmo salar smolts

This study provides the first direct observations that photoperiod controls the initiation of downstream movement in Atlantic salmon Salmo salar smolts. Under simulated natural day length (LDN) conditions and seasonal increases in temperature, smolts increased their downstream movements five-fold for a period of 1 month in late spring. Under the same conditions, parr did not show changes in downstream movement behaviour. When given a shortened day length (10L:14D) beginning in late winter, smolts did not increase the number of downstream movements. An early increase in day length (16L:8D) in late winter resulted in earlier initiation and termination of downstream movements compared to the LDN group. Physiological status and behaviour were related but not completely coincident: gill Na + /K + -ATPase activity increased in all treatments and thyroid hormone was elevated prior to movement in 16L:8D treatment. The most parsimonious model describing downstream movement of smolts included synergistic effects of photoperiod treatment and temperature, indicating that peak movements occurred at colder temperatures in the 16L:8D treatment than in LDN, and temperature did not influence movement of smolts in the 10L:14D treatment. The complicated interactions of photoperiod and temperature are not surprising since many organisms have evolved to rely on correlations among environmental cues and windows of opportunity to time behaviours associated with life-history transitions. These complicated interactions, however, have serious implications for phenological adjustments and persistence of S . salar populations in response to climate change.

Journal of Fish Biology↗