Benjamin Marcy-Quay

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.

Species 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.

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.

Obtaining robust estimates of population abundance is a central challenge hindering the conservation and management of many threatened and exploited species. Close‐kin mark‐recapture (CKMR) is a genetics‐based approach that has strong potential to improve the monitoring of data‐limited species by enabling estimates of abundance, survival, and other parameters for populations that are challenging to assess. However, CKMR models have received limited sensitivity testing under realistic population dynamics and sampling scenarios, impeding the application of the method in population monitoring programs and stock assessments. Here, we use individual‐based simulation to examine how unmodeled population dynamics and aging uncertainty affect the accuracy and precision of CKMR parameter estimates under different sampling strategies. We then present adapted models that correct the biases that arise from model misspecification. Our results demonstrate that a simple base‐case CKMR model produces robust estimates of population abundance with stable populations that breed annually; however, if a population trend or non‐annual breeding dynamics are present, or if year‐specific estimates of abundance are desired, a more complex CKMR model must be constructed. In addition, we show that CKMR can generate reliable abundance estimates for adults from a variety of sampling strategies, including juvenile‐focused sampling where adults are never directly observed (and aging error is minimal). Finally, we apply a CKMR model that has been adapted for population growth and intermittent breeding to two decades of genetic data from juvenile lemon sharks (Negaprion brevirostris) in Bimini, Bahamas, to demonstrate how application of CKMR to samples drawn solely from juveniles can contribute to monitoring efforts for highly mobile populations. Overall, this study expands our understanding of the biological factors and sampling decisions that cause bias in CKMR models, identifies key areas for future inquiry, and provides recommendations that can aid biologists in planning and implementing an effective CKMR study, particularly for long‐lived data‐limited species.

Kinship‐based methods of population assessment such as close‐kin mark‐recapture require accurate and efficient genotyping methods capable of resolving complex relationships among kin. Inference of such relationships can be difficult using biallelic loci due to the large number of markers required to obtain the necessary power. Sequencing‐based microsatellite panels offer an efficient alternative, combining high polymorphism with efficient next‐generation methods. Here we construct, optimize, and test one such panel for lake trout (Salvelinus namaycush) using a combination of previously‐published loci adapted for sequencing and de novo loci mined from a genome assembly. We performed three rounds of primer optimization, yielding a final panel of 131 loci, followed by testing with two different levels of PCR multiplexing (all primers in one or two groups) and two different reaction volumes (5 and 10 μL). Our results showed that the use of the largest multiplex and smallest reaction volume did not substantially change results, allowing significant cost and time savings. To test panel accuracy, we used both a set of 153 known‐origin samples from origins of management interest and a series of hatchery crosses representing nine families with parent‐offspring, half‐sibling, and largely‐unrelated pairs. Our results indicate that sequencing‐based microsatellite panels can efficiently and accurately provide the information required for a population genetics analyses including population assignment, calculation of between‐population F_ST, and kinship‐based population estimation techniques. Such techniques are seeing increasing applications for a wide range of taxa; our findings should provide insight and guidance for the development of the necessary molecular resources.

The population of Lake Trout Salvelinus namaycush in Lake Champlain has been sustained by stocking since 1973, but natural recruitment of wild fish has been observed since 2012. By 2020, continued recruitment and maturation of wild year-classes indicated that updated population parameters were needed to assess and adjust management practices. Age estimation from historical methods (fin clips and scales) was undependable due to crowding of annuli in older fish and the inability to verify uncertain age estimates using a 5-year fin clip rotation for older fish. We used maxillary bones to obtain precise and accurate age estimates for adult wild and stocked fish. In combination with preadult ages derived from fin clips and length–frequency analysis, we estimated the contemporary survival and growth of juvenile (age 2–3), early-adult (age 3–4), and adult (age 5+) Lake Trout in Lake Champlain. The precision and accuracy of our maxillary age estimates were greater than or comparable to the precision and accuracy of otolith and maxillary age estimates of Lake Trout populations in the Great Lakes. Estimates of Lake Trout growth suggested that stocked and wild fish grew at different rates, with stocked fish having an early size advantage but ultimately reaching a similar maximum size. There were no significant differences in length–weight relationships between stocked and wild fish. Estimates of adult survival were slightly greater than range-wide averages and well above recent estimates for stocked populations in the Great Lakes. Juvenile and early-adult survival estimates were similar to each other and both far lower than adult estimates. Stocked and wild fish had similar survival rates in all age-classes. Ultimately, the use of maxillary bones allowed us to make better estimates of contemporary population parameters necessary for informing management decisions.

Consistently repeated daily habitat shifts by fish can expose or protect individuals from a variety of threats and influence nutrient transport between systems, yet logistical constraints make individual horizontal movement difficult to study on short time scales. As a result, diel movements by fish are often poorly documented. Suckers (Catostomidae) are a key group of fish that have been frequently examined with this in mind, as many species are large, long-lived, and comprise a large proportion of biotic biomass in many waters. Previous studies in rivers have shown that multiple sucker species exhibit complex, diel movement. We investigated the prevalence of short-term movement by the widely distributed Catostomus commersonii (White Sucker) in an interconnected, remote lake system within New York's Adirondack region using PIT telemetry. These 2 lakes were in a remote setting of New York's Adirondacks, and our tracking studies indicated a subset of the sucker population regularly traveled back and forth daily through a short, shallow channel. Direction of movement was strongly associated with time of day, and larger individuals were far more likely to engage in this repetitive behavior. Overall, these findings highlight the potential for extensive, yet generally unobserved, movement by White Suckers within connected lake systems.