Geology topics

Benjamin Marcy-Quay

Publications and source records attributed to Benjamin Marcy-Quay.

9 recordsLinked to original sources

USGS2026

Estimation of parental abundance using hierarchical Bayesian modeling with data augmentation

Pedigree-based estimation methods leverage the fact that each offspring in a cohort is genotypically “marked” by its parents and represent a recent and promising toolset for estimating population dynamics. This includes pedigree accumulation estimators that model the “accumulation” of inferred unique parents within a given cohort to estimate parental abundance. Unlike close-kin mark-recapture approaches, which rely on intercohort comparisons, pedigree accumulation modeling can be completed solely using intracohort samples. This is particularly advantageous for semelparous species, where intercohort pairs are impossible and adult life stages can be difficult to sample without affecting their likelihood of successfully reproducing. Previous work has evaluated a range of estimators for such datasets, concluding that the non-parametric Chao estimator provides the most accurate and precise estimates for feasible levels of sampling effort. We used simulated data to evaluate an alternative estimator based on hierarchical modeling and data augmentation in a Bayesian framework. Results indicate that estimates from the hierarchical Bayesian estimator had comparable accuracy and better precision than both the previously tested Chao1 estimator and the improved iChao formulation across a range of sample sizes and sex ratios. Furthermore, the Bayesian estimator was far more robust to simulated errors in pedigree reconstruction, especially the presence of false negatives. Hierarchical Bayesian pedigree accumulation models can also provide additional insight into underlying reproductive ecology through their use of an explicit observation process, allowing for the incorporation or estimation of species- and population-specific reproductive dynamics. More broadly, the parametric nature of these models offers opportunities to efficiently pool information among datasets as well as to propagate uncertainty within more complex models.

Ecology and Evolution↗

USGS2025

Eradication efforts catalyze rapid evolution in an invasive predatory fish

pecies invasions spur costly and labor-intensive control efforts, yet even local eradication is seldom achieved. When control measures are initially effective, they may drive evolutionary adaptation that prevents full eradication, as has been documented for some chemical and biocontrol approaches. Although the intensity, directionality, and persistence of selection required to increase the frequency of resistant genotypes in complex natural ecosystems remains an open question, theory predicts that high mortality can cause life-history evolution even in the absence of a strong selective agent. Here, we use annually collected ecological and genetic data to show that rapid evolution of introduced smallmouth bass has undermined a 20-y manual suppression effort in a mid-sized lake. Despite nearly doubling annual mortality, our intensive control program produced a larger bass population dominated by young and early-maturing fish. These shifts were accompanied by large allele frequency changes in three genomic regions associated with earlier maturation and increased somatic growth. Our findings bear out the theoretical prediction that high mortality can drive evolutionary adaptation in target species. Controlling species invasions are worldwide practices that typically remove a substantial proportion of a population during each of many successive generations, hence life history adaptation may be commonplace. Such evolutionary responses could be salient in explaining the widespread failure of invasion control efforts. Genetic and phenotypic monitoring to detect cryptic adaptation and preemptive design of invader eradication programs to deliberately disrupt directional selection for resistance could improve invasion control outcomes.

New York↗

USGS2025

Tourists or residents? Life history strategies of Rainbow Smelt in Lake Champlain

Objective Rainbow Smelt Osmerus mordax are the most important native prey fish in the coldwater food web of Lake Champlain, but their history in the lake is not well understood. Writers in the 1800s described a nonresident population of smelt that reached sizes greater than 315 mm that was sympatric with a population of individuals that matured at smaller sizes. No studies, however, have investigated mechanisms that cause the dimorphic size structure of Rainbow Smelt in Lake Champlain. Based on our results, larger fish appear to have life history strategy differences from most of the population, which allow them to grow to larger sizes, faster. We proposed three alternative hypotheses to explain the presence of these large Rainbow Smelt in Lake Champlain: (1) anadromous and landlocked Rainbow Smelt may both be present in the lake, (2) all Rainbow Smelt may be landlocked with the two morphotypes resulting from different diet preferences and/or differences in environmental niche occupancy, or (3) the largest Rainbow Smelt are long-lived and therefore had longer time for growth. Methods We tested these hypotheses using otolith microchemistry, diet (stomach content and stable isotope), and age analyses. Our length-at-age analyses showed that age structure was not bimodal, but there are fish present in the lake as large as those in the 1800s. Results Microelemental analysis indicated that Rainbow Smelt in Lake Champlain were landlocked, with no marine signature. Stomach contents of average-sized Rainbow Smelt were exclusively zooplankton and macroinvertebrates, while the larger Rainbow Smelt were primarily piscivorous and had greater δ 15 N values, which suggests a higher trophic position. A combination of hypotheses 2 and 3 most likely explains current population structure. Elevated manganese : magnesium ratios in larger Rainbow Smelt suggest that they may utilize a hypoxic environmental niche, a potential key life history strategy allowing for faster growth, suggesting that there may be intraspecific variation in how Rainbow Smelt use the basins of Lake Champlain. Conclusions Based on our results, larger fish appear to have life history strategy differences from most of the population that allow them to grow to larger sizes, faster. Future studies are needed to uncover the nuances of the mechanisms for growth.

New York, Vermont↗

USGS2025

Sea Lamprey control reduction during the COVID-19 pandemic corresponds to rapid increase in Sea Lamprey abundance

The Sea Lamprey Petromyzon marinus control program in the Laurentian Great Lakes is one of the longest-running and most successful invasive species suppression programs in the world. Although several techniques are used to suppress Sea Lamprey, the control program relies heavily on regular application of lampricide to kill stream-dwelling larvae. The COVID-19 pandemic disrupted lampricide application from 2020 to 2022, which provided a unique opportunity to test how Sea Lamprey populations and wound counts on fishes would respond. We evaluated the consequences of decreased control effort at a basin-wide level using standard control program metrics and through a focused analysis of multispecies wounding in Lake Ontario, which experienced the greatest disruption in Sea Lamprey control. The reduction in control effort corresponded to increased basin-wide adult Sea Lamprey abundance but was only weakly associated with Lake Trout Salvelinus namaycush wounding. However, the novel multispecies wounding rate metric calculated for Lake Ontario increased and was consistent with observations by anglers and managers regarding a sharp increase in Sea Lamprey abundance following reduced effort. Ultimately, our research highlights that consistent treatment is critically important for preventing damage stemming from Sea Lamprey and that reductions in suppression could quickly lead to a resurgence in abundance.

Great Lakes↗

USGS2025

Evaluation of a recovering lake trout population in Lake Champlain using close-kin mark-recapture and genetic strain assignment

Lake trout ( Salvelinus namaycush ) populations in many northern North American large lake systems have been substantially reduced or extirpated due to overfishing, habitat loss, and introduction of invasive species. Following reductions in fishing pressure and successful suppression of sea lamprey, attempts have been made to restore self-sustaining populations into most of these waters but success has been slow and limited. In contrast, lake-wide lake trout restoration occurred abruptly and rapidly in Lake Champlain after 40 years of stocking, with robust, widespread, and sustained wild recruitment observed from the 2012 cohort onwards. We sought to better understand the dynamics of the recovery success in Lake Champlain using a multi-year tissue dataset, in combination with a recently-designed genotyping panel and close-kin mark-recapture, to quantify the performance (i.e., survival and reproductive success) of stocking sources and strategies with an eye towards informing restoration programs in other systems. We also assessed the overall abundance of adult fish and parental dynamics associated with wild recruitment. Our results indicate that adult survival is remarkably high and overall abundance is low compared to other large lake systems in similar latitudes, with the vast majority of wild recruitment genetically traceable to the Seneca strain fish historically stocked by New York State. We observed little evidence of hybridization between the two strains and close-kin mark-recapture estimates indicated that approximately 20 % of the adult population was contributing to successful recruitment on a regular basis. Ultimately, our results point to a growing wild population that has the potential to become self-sustaining.

New York, Vermont↗

USGS2024

Lake Trout (Salvelinus namaycush) origin, behavior, and habitat residency in Sherbrooke Lake, Nova Scotia, Canada

The southeastern edge of the Lake Trout ( Salvelinus namaycush ) range extends to Nova Scotia (NS), Canada, including Sherbrooke Lake, Lunenburg County. These Lake Trout may be of native origin; however, the putatively native population was historically supplemented by stocking from nonindigenous strains. To determine genetic origin of this population, 25 Lake Trout from Sherbrooke Lake were used to compare genetic likeness to populations that had been stocked into the lake. Lake Trout of Sherbrooke Lake were determined to be highly genetically distinct from source populations in Ontario, Manitoba, New York, and Vermont, suggesting that the extant population is of native origin. To identify suitable habitat of Lake Trout in Sherbrooke Lake, acoustic telemetry was used to track the depth and temperature residency of 11 Lake Trout in tandem with measuring lake bathymetric and water column temperature and oxygen. During spring and summer, 2022, Lake Trout occupied a hypolimnetic residency, ranging from 11 to 22 m of depth and 8.5 to 10.0 °C. Suitable conditions for Lake Trout were available in the south basin. The main basin, containing ~ 80% of the lake’s volume, was unstratified and unsuitable for Lake Trout. The effects of Hurricane Fiona caused the hypolimnion in the south basin to shrink via the thermal mixing of the epilimnion, forcing adult Lake Trout to a depth range of 16–18 m for ~ 1 month. During this time, suitable Lake Trout habitat comprised only ~ 0.5% of the total volume of Sherbrooke Lake.

Nova Scotia↗

USGS2023

Parentage-based tagging using mothers balances accuracy and cost for discriminating between natural and stocked recruitment for inland fisheries

Hatchery programmes are frequently used to supplement inland fisheries, yet achieving successful management outcomes often requires information on stocked versus naturally reproduced fish abundance. Parentage-based tagging – genetically assigning offspring to their parents – has potential to be an effective approach for distinguishing stocked and naturally reproduced fish. However, several challenges may limit its application to inland fisheries, including genetic relatedness among populations that can affect identification accuracy and high costs of genotyping large broodstocks. Here, we demonstrate the efficacy of parentage-based tagging based on broodmothers in the Lake Ontario Chinook Salmon fishery, which uses thousands of broodparents and has potential for substantial relatedness between stocked and naturally reproduced fish. Restricting parent sampling to broodmothers reduced costs by two-thirds, was logistically pragmatic, and achieved >95% accuracy in distinguishing stocked from naturally reproduced salmon. Combined, these results highlight the potential wide applicability of parentage-based tagging for assessing stocking programmes in inland waters.

New York, Ontario↗

USGS2020

Expanding the feasibility of fish and wildlife assessments with close-kin mark–recapture

Close-kin mark–recapture (CKMR) is a powerful new method for the assessment of fish and wildlife population dynamics. Unlike traditional mark–recapture techniques, the use of kinship as an identifying mark is robust to many forms of capture heterogeneity including variation in gear efficiency and tagging-based effects such as loss and differential mortality. In addition, close-kin methods can be applied to a wider range of sampling designs than traditional methods (e.g., single-occasion surveys and lethal capture), can provide retrospective historical abundance estimates, and can produce survival estimates from as few as two sampling occasions. We evaluated the ability of CKMR to provide estimates of abundance and adult survival and then compared results to those from traditional mark–recapture. This analysis incorporated data from a three-year study of lake resident brook trout ( Salvelinus fontinalis ) where individuals were both physically (PIT) tagged and genotyped for 44 de novo developed microsatellites with high throughput sequencing. Traditional mark–recapture estimates were derived using Pollock’s Robust Design, relying upon three primary open sampling occasions and four secondary closed occasions. We found that close-kin methods produced contemporary estimates of adult abundance and survival that were similar to those produced by traditional mark–recapture in both magnitude and precision. Furthermore, CKMR provided abundance estimates for multiple years prior to sampling and, when restricted to data from a single year, still produced reliable abundance estimates for at least one and as many as three years. Retrospective abundance estimates corresponded with those from a separate historical two-sample mark–recapture dataset. This study provides support for the use of CKMR as a robust and sampling-efficient alternative to traditional mark–recapture methods of assessing population parameters.

New York↗

USGS2020

Seasonal habitat use indicates that depth may mediate the potential for invasive round goby impacts in inland lakes

The round goby ( Neogobius melanostomus ) is among the fastest-spreading introduced aquatic species in North America and is radiating inland from the Great Lakes into freshwater ecosystems across the landscape. Predicting and managing the impacts of round gobies requires information on the factors influencing their distribution in habitats along the invasion front, yet this information is not available for many recently invaded ecosystems. We evaluated the seasonal habitat use and biomass of round gobies in an inland temperate lake to define the spatiotemporal scope of biological interactions at the leading edge of the round goby invasion. Using novel statistical approaches, we combined hierarchical models that control for imperfect species detection with flexible smooth terms to describe non-linear relationships between round goby abundance and environmental gradients. Subsequently, we generated accurate detection-corrected estimates of the standing stock biomass of round gobies. Our results show seasonally differentiated habitat niches, where suitable round goby habitat in summer months is restricted to shallow depths (<18.4 m) with a mixture of vegetative and mussel cover. We found high round goby biomass of 122 kg/ha in occupied habitats during the summer, with a total lake-wide biomass of 766,000 kg. In winter, round gobies migrate to deep offshore habitats and disperse, dramatically altering their scope for biological interactions with resident aquatic species across summer and winter seasons. The results of this study indicate that the scope of biological interactions in inland lakes may be seasonally variable, with potential for high round goby biomass in shallow lakes or at the periphery of deep lakes in the summer months. Such shallow-water habitats may therefore present higher risk of ecological impacts from round gobies in invaded lentic ecosystems. As round gobies expand inland, consideration of seasonal habitat use will be an important factor in predicting the impacts of this pervasive invader.

New York↗