Geology topics

Nicholas M. Sard

Publications and source records attributed to Nicholas M. Sard.

7 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

Reproductive contribution of lake sturgeon transferred upstream of dams on a Great Lakes tributary

Dam construction contributes to declines in the distribution and abundance of many fishes. Increasing connectivity through adult transfer can be demographically and genetically beneficial, but assessing the effects resulting from transfer can be difficult if resident fish exist upstream. Genotypes of adult and larval lake sturgeon ( Acipenser fulvescens ) were used to quantify contributions to larval recruitment from adults transferred upstream of dams on the Menominee River, USA. We evaluated whether transfer timing, sex, and adult size were associated with the odds of reproduction. Elevator transfer operations in Fall 2019, Fall 2020, and Spring 2021 resulted in 152 male and 81 female lake sturgeon transferred upstream. In 2020 and 2021, 580 and 518 larvae were genotyped. We found that 86% (201/233) of adults reproduced and 62.3% (684/1098) of offspring had transferred parents. In total, we estimated that 392 resident adults contributed to offspring production. Mixed matings accounted for 53% of offspring genotyped, increasing levels of offspring genetic diversity relative to offspring produced from resident-only matings. Transferring adults may be a viable restoration alternative for other iteroparous fish in river systems where connectivity to spawning areas has been impeded.

Michigan, Wisconsin↗

USGS2024

Genomic data characterize reproductive ecology patterns in Michigan invasive Red Swamp Crayfish (Procambarus clarkii)

The establishment and spread of invasive species are directly related to intersexual interactions as dispersal and reproductive success are related to distribution, effective population size, and population growth. Accordingly, populations established by r-selected species are particularly difficult to suppress or eradicate. One such species, the red swamp crayfish ( Procambarus clarkii ) is established globally at considerable ecological and financial costs to natural and human communities. Here, we develop a single nucleotide polymorphism (SNP) loci panel for P. clarkii using restriction-associated DNA-sequencing data. We use the SNP panel to successfully genotype 1800 individuals at 930 SNPs in southeastern Michigan, USA. Genotypic data were used to reconstruct pedigrees, which enabled the characterization of P. clarkii's mating system and statistical tests for associations among environmental, demographic, and phenotypic predictors and adult reproductive success estimates. We identified juvenile cohorts using genotype-based pedigrees, body size, and sampling timing, which elucidated the breeding phenology of multiple introduced populations. We report a high prevalence of multiple paternity in each surveyed waterbody, indicating polyandry in this species. We highlight the use of newly developed rapid genomic assessment tools for monitoring population reproductive responses, effective population sizes, and dispersal during ongoing control efforts.

Evolutionary Applications↗

USGS2024

Demographic patterns of walleye (Sander vitreus) reproductive success in a Wisconsin population

Harvest in walleye Sander vitreus fisheries is size-selective and could influence phenotypic traits of spawners; however, contributions of individual spawners to recruitment are unknown. We used parentage analyses using single nucleotide polymorphisms to test whether parental traits were related to the probability of offspring survival in Escanaba Lake, Wisconsin. From 2017 to 2020, 1339 adults and 1138 juveniles were genotyped and 66% of the offspring were assigned to at least one parent. Logistic regression indicated the probability of reproductive success (survival of age-0 to first fall) was positively (but weakly) related to total length and growth rate in females, but not age. No traits analyzed were related to reproductive success for males. Our analysis identified the model with the predictors' growth rate and year for females and the models with year and age and year for males as the most likely models to explain variation in reproductive success. Our findings indicate that interannual variation (i.e., environmental conditions) likely plays a key role in determining the probability of reproductive success in this population and provide limited support that female age, length, and growth rate influence recruitment.

Wisconsin↗

USGS2023

Field and laboratory validation of new sampling gear to quantify coregonine egg deposition and larval emergence across spawning habitat gradients

The influence of habitat and environmental conditions on Great Lakes coregonine reproduction is not well described, in part, because we lack sampling gears for early life stages that are effective across habitats. We designed new egg and larval emergence traps to quantify coregonine reproductive success across variable depths and substrates and tested them in laboratory and field settings. In the laboratory, our new metal ring egg traps had greater egg retention (94–100%) and faster post-catch processing (5–7 min) relative to a commonly employed fiber mat trap (30–67% and 30–60 min). In Lake Ontario’s Chaumont Bay, egg densities for lake whitefish Coregonus clupeaformis (0–5,832 eggs m −2 ) and cisco Coregonus artedi (0–426,501 eggs m −2 ) measured with metal ring traps (n = 112) varied across habitats but were greatest between 2–5 m on rock and dreissenid mussel substrates. Emergence traps used an inverted cone, fine mesh, and a clear collection chamber to capture positively phototactic emerging larvae. In the laboratory, traps captured 69–80% of emerged larvae. In Chaumont Bay, emergence traps deployed for 21 days after ice out caught only cisco larvae. Emergence rates varied across habitats (0–118 larvae m −2 day −1 , n = 85) but were highest on dreissenid mussel reef substrate. Our samplers improved processing efficiency and facilitated large sample sizes to quantify variability in egg deposition densities and emergence rates across habitats. These methods can advance coregonine conservation by determining how anthropogenic changes to habitat and environmental conditions influence incubation success.

Journal of Great Lakes Research↗

USGS2022

Contemporary spatial extent and environmental drivers of larval coregonine distributions across Lake Ontario

Coregonine fishes are important to Laurentian Great Lakes food webs and fisheries and are central to basin-wide conservation initiatives. In Lake Ontario, binational management objectives include conserving and restoring spawning stocks of cisco ( Coregonus artedi ) and lake whitefish ( C. clupeaformis ), but the spatial extent of contemporary coregonine spawning habitat and the environmental factors regulating early life success are not well characterized. In Spring 2018, we conducted a binational ichthyoplankton assessment to describe the spatial extent of coregonine spawning habitat across Lake Ontario. We then quantified the relative importance of a suite of biophysical variables hypothesized to influence coregonine early life success using generalized additive mixed models and multimodel inference. Between April 10 and May 14, we conducted 1,092 ichthyoplankton tows and captured 2,350+ coregonine larvae across 17 sampling areas, predominantly within embayments. Although 95% of catches were in the eastern basin, coregonine larvae were also found in historical south shore spawning areas. Most coregonine larvae were cisco; <6% were lake whitefish. Observed catches of both species across sampling areas were strongly and similarly associated with ice cover duration, but the importance of site-specific characteristics varied, such as distance to shore and site depth for cisco and lake whitefish, respectively. These results suggest that regional-scale climatic drivers and local environmental habitat characteristics interact to regulate early life stage success. Furthermore, strong regional and cross-species variation in larval distributions emphasize the importance of lake-wide assessments for monitoring both the current eastern basin populations and potential expansions into western Lake Ontario habitats.

Lake Ontario↗

USGS2021

Pedigree accumulation analysis: Combining methods from community ecology and population genetics for breeding adult estimation

Estimates of the number of successfully breeding adults ( N S ) in a population can predict levels of recruitment. However, assessments of N S are often difficult to obtain because encounters with adults are limited due to life-history characteristics, low abundance or other constraints associated with access to critical habitats. Alternatively, efforts to sample individuals at earlier ontogenetic stages can be more tractable, resulting in more comprehensive samples. To estimate N S , we describe, evaluate and apply two nonparametric species richness estimators to information associated with genetic pedigree reconstruction. Simulations compared bias and precision associated with Chao and Jackknife methods when estimating N S . We also evaluated N S estimation sensitivity to two sources of variation associated with species reproductive ecology (variance in reproductive success and sex ratio skew) and genetic pedigree assignment error. Finally, the application of our novel method was demonstrated in two different species and systems (Chinook Salmon in Oregon, USA and Lake Sturgeon in Michigan, USA). We found unbiased N S estimates were generated across a broad range of offspring sample sizes using the Chao method. Empirical results corroborated simulation-based expectations and highlighted applications where parents and offspring are sampled, and when only offspring are sampled. When offspring sample sizes are adequate and pedigree reconstruction errors are low, the combination of established methods from community ecology and genetic pedigree reconstruction provides an accurate alternative method to estimate N S that can facilitate population assessments.

Methods in Ecology and Evolution↗