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Amanda Susanne Ackiss

Publications and source records attributed to Amanda Susanne Ackiss.

At least 19 recordsLinked to original sources
USGS2026

Two hundred years of historical spawning and nursery data for coregonine fishes in the Laurentian Great Lakes

Historical data can provide critical ecological information for species across the globe, many of which are facing unprecedented rates of ecosystem change. Yet, historical information related to freshwater species, especially fishes, remains scattered, often in original formats, and underutilized for informing conservation and restoration activities. Here, we present a Data Descriptor called Coregonine Spawning History (CORHIST), a database designed to house diverse data related to past spawning and nursery areas for fishes in the family Salmonidae, subfamily Coregoninae (ciscoes and whitefishes), in the Laurentian Great Lakes and their tributaries. Data for 11 species of coregonines historically occurring in the Great Lakes are included in CORHIST. Over 3,400 occurrence records at the coordinate scale have been entered, over 2,200 of which are for Cisco ( Coregonus artedi ) and Lake Whitefish ( C. clupeaformis )—two focal species for which there is either multinational conservation interest or restoration efforts underway in the Laurentian Great Lakes. CORHIST is already proving useful for several studies developing habitat suitability models and delineating spatial units for conservation or restoration planning.

Laurentian Great Lakes↗
USGS2026

Epigenetics in captivity: Restoring wild phenotypes in captive-reared salmonids

Captive rearing is a common practice for the stocking, conservation, and supplementation of fish species worldwide, but captive-reared fish can exhibit altered phenotypes leading to reduced fitness in nature compared to wild conspecifics. In salmonids, certain studies have found limited genetic differentiation between wild and captive-reared fish. However, documented changes in gene expression in hatchery fish have led scientists to investigate epigenetic mechanisms, such as DNA methylation, as a source of these differences. In this binational collaborative piece, we synthesize the knowledge and efforts of academics and government scientists to highlight how interactions between captive rearing and the epigenome elicit parallel phenotypic changes across salmonid species. We examine the known and potential links between DNA methylation and the phenotypic effects of captive rearing including changes in behavior, color, gut microbiomes, and developmental abnormalities. We review efforts to minimize these phenotypic and epigenetic effects including attempts to modify the hatchery environment and rearing protocols. We provide a framework to integrate epigenetic considerations into hatchery rearing protocols by weighing the heritable nature of DNA methylation with the goals of different captive rearing programs and explore whether minimizing the phenotypic and epigenetic effects of captive rearing is worthwhile. We examine heritability and persistence of epigenetic effects, and we propose the exploitation of heritable bet-hedging as an epigenetic buffer to increase post-release survival. We also suggest novel applications of epigenomic biomarkers as a non-lethal method for post-release monitoring. Ultimately, collaborative multi-disciplinary research across species is needed to understand the comprehensive effects of captive rearing, reduce the ecological impacts of captive fish in the wild, and increase population resilience. Integrating epigenetics into fish hatchery management will provide new opportunities for optimizing and improving captive rearing.

Evolutionary Applications↗
USGS2026

Spatial units to support Lake Erie Cisco Coregonus artedi restoration

At the request of the Lake Erie Committee, spatial units for Lake Erie Cisco were delineated during spring 2024. Spatial units correspond to the reproductive habitat of extirpated (unoccupied spatial units) and extant (occupied spatial units) populations. Spatial units were delineated using a Council of Lake Committees-endorsed method that involves synthesizing data for evaluation by a panel with expertise on the focal organisms and ecosystems. By examining catch, survey, observational, and genetic data, an expert panel determined that no viable Cisco populations remain in Lake Erie. Experts delineated one eastern and one western unoccupied Cisco spatial unit in Lake Erie based on interpretation of historical movement and spawning locations and timing. The expert panel also identified eleven key questions that can be investigated to further inform Lake Erie Cisco restoration. The two unoccupied spatial units will form the basis of a follow-on threats assessment and population viability models that together provide fishery managers science-based planning tools for Lake Erie Cisco restoration.

Lake Erie↗
USGS2026

Describing the seasonal abundance and growth rates of larval fishes across productivity gradients in Lake Huron in 2017

Several of the Laurentian Great Lakes, including Lake Huron, have undergone oligotrophication in the past decades and prey fish biomass has concomitantly declined. One potential mechanism to explain declines in prey fish is slower growth and lower survival at the larval stage. To determine whether reduced productivity affects the growth of larval fish, we sampled larval fishes and their environment approximately monthly from May through August 2017 at nine nearshore to offshore transects across Lake Huron that included North Channel, Georgian Bay, and the main basin. North Channel transects had the highest chlorophyll a concentrations and zooplankton densities. Rainbow smelt ( Osmerus mordax ), burbot ( Lota lota ), bloater ( Coregonus hoyi ), and shiners ( Notropis spp.) were the most abundant larval fish taxa, peaking in June and July. We aged rainbow smelt and bloater using otoliths, and estimates of growth rate revealed rainbow smelt always grew faster. For both species, we explained variation in total length by comparing 16 candidate linear mixed-effects models, with age, chlorophyll a , zooplankton, water temperature, larval fish density, and interactions with age as predictor variables. For rainbow smelt, the full model was best; zooplankton had the greatest effect, but it was negative and opposite from our hypothesis. For bloater, four candidate models were most parsimonious; water temperature had the greatest effect, and it was positive as predicted from our hypothesis. To more effectively evaluate whether zooplankton can limit larval fish growth and survival, we recommend that future designs conduct more frequently sampling within a year even at the expense of fewer transects.

Lake Huron↗
USGS2026

A genomic tool to tackle cryptic diversity demonstrates the potential for off-target use of GT-seq panels

A comprehensive understanding of life history is vital to successful species conservation and management. When different life history stages are accompanied by considerable morphological or cryptic variation, such as the egg and larval phases exhibited by most fishes, genomic tools are essential for identifying species so that early-life ecology questions can be studied. Genotyping-in-thousands by sequencing (GT-seq) has recently emerged as a targeted and efficient approach for species identification. We leveraged existing genomic and transcriptomic data to develop a GT-seq panel capable of differentiating the members of the Coregonus artedi complex, a radiation of salmonids in the Laurentian Great Lakes whose members are indistinguishable with mitochondrial DNA barcoding loci and are the focus of bi-national conservation initiatives. Our panel of 494 loci was able to assign fishes in the C. artedi complex to species and lake. We examined cross-amplification in other coregonines with overlapping distributions and found that congeneric Lake Whitefish ( C. clupeaformis ) cross-amplified at 94% of loci and confamilial Round and Pygmy Whitefish ( Prosopium spp.) cross-amplified at 42% and 38% of loci, respectively. We adapted bioinformatic probes to account for Prosopium -specific variants including 22 new SNPs and developed a whitelist of 428 SNPs capable of distinguishing these whitefishes. Finally, we demonstrated performance by identifying 3,066 coregonine larvae and juveniles collected in spring 2019-2021 from Lake Superior. These results hold promise for future insights into the species-specific ecology of early life coregonines and demonstrate the flexibility of GT-seq panels, which may cross-amplify hundreds of informative genome-wide loci in related taxa.

BioRxiv↗
USGS2025

Day versus night relations between larval lake whitefish, cisco, and zooplankton onshore in Lakes Michigan, Huron, and Superior

Lake whitefish ( Coregonus clupeaformis ) populations in the upper Great Lakes have undergone declines in the past two decades, particularly in Lakes Michigan and Huron. However, cisco ( Coregonus artedi ) are recovering in parts of the Great Lakes. Population declines are hypothesized to be due, in part, to reduced zooplankton prey in areas that serve as critical habitat for larval coregonines. Larval lake whitefish, cisco, and zooplankton are commonly sampled only during daylight hours. Habitat use, community composition, catch rates, and abundance estimates of larval fish and zooplankton can change drastically at night versus day, necessitating diel comparisons for a more comprehensive understanding of the early life history of coregonines and their prey. We collected paired day and night onshore (≤ 1 m depth) zooplankton and larval coregonine samples from Lakes Michigan, Huron, and Superior in March–June 2021 to test if there were diel differences in lake whitefish and cisco abundance and zooplankton density and biomass. We also tested if relationships exist between larval coregonine abundance and zooplankton density and biomass and environmental variables (water temperature, dissolved oxygen concentration, pH, specific conductivity, substrate type). We observed consistently higher zooplankton density and biomass and larval lake whitefish and cisco abundance at night. Larval coregonine abundance was positively related to higher zooplankton population estimates but was not related to the environmental variables measured. Our results provide insight into sampling practices for larval lake whitefish, cisco, and zooplankton onshore in the Great Lakes to better understand factors influencing larval lake whitefish and cisco recruitment.

Michigan↗
USGS2025

Drowned river mouth lakes are winter foraging habitats for the expanding Lake Michigan cisco Coregonus artedi population

Characterizing fish movements is required for understanding habitat use, energy flow, and trophic structure and can inform fisheries management. Drowned river mouth (DRM) lakes are productive inland habitats in the Laurentian Great Lakes basin used by migratory fishes. Despite recognition of their ecological connections to the Great Lakes, the value of DRM lakes as seasonal habitats is not well understood for many fishes. One such species, cisco Coregonus artedi , has recently expanded in Lake Michigan from near extirpation to higher relative abundances in the northeastern portion of the lake. Cisco are recreationally harvested in some DRM lakes during winter, but little is known about cisco movement patterns and ecology. In winter 2022 and 2023, we collected cisco from three DRM lakes along the eastern shores of Lake Michigan (Lake Charlevoix, Portage Lake, Muskegon Lake) to characterize genetics, morphometrics, and diets. We also implanted telemetry tags in 20 cisco collected in Lake Charlevoix to examine movement patterns and determine DRM lake residency (i.e., seasonal vs. year-round). We found no consistent genetic or morphometric differentiation across DRM lakes, suggesting that recolonization began from a single stock. Fish were the only diet item found in cisco guts collected during winter months. Movement patterns from Lake Charlevoix indicated strong spawning site fidelity to Grand Traverse Bay as well as non-spawning site fidelity. However, given the presence of cisco in southern DRM lakes and some site-specific differences in morphometrics, managers could benefit from further research to determine whether spawning occurs in southern Lake Michigan.

Journal of Great Lakes Research↗
USGS2025

Lake Ontario spring prey fish bottom trawl survey and Alewife assessment, 2025

The multi-agency Lake Ontario spring prey fish survey quantifies changes in pelagic prey fish populations, in particular Alewife Alosa pseudoharengus , which are the primary prey supporting the lake’s sport fishes. The 2025 survey included 230 trawls in the main lake and embayments and sampled depths from 5.5 to 245 m (15 – 810 ft). The survey captured 504,541 fish from 33 species with a total weight of 7,301 kg (16,095 lbs). Alewife were 85% of the total catch numerically, while Yellow Perch Perca flavescens , Round Goby Neogobius melanostomus , Deepwater Sculpin Myoxocephalus thompsonii , and Rainbow Smelt Osmerus mordax , comprised 5%, 4%, 3%, and 1% of the catch, respectively. The Alewife biomass index decreased from 2024 to 2025 (83 to 78 kg·ha -1 ) however due to an abundant 2024 Alewife year class the density index increased from 3,727 to 9,182 fish per ha -1 . The Age-1 biomass (2024 year class) was 27.5 kg·ha -1 , which was the greatest value estimated in the modern time series (since 1997). The abundance estimate for the 2024 Alewife year class (13.8 billion) was more than three times the number of all other Alewife combined (3.6 billion). Adult Alewife abundance decreased in 2025 which was consistent with predictions from 2024. Those predictive models suggested that adult Alewife biomass is likely to increase in 2026 and 2027, as the 2024 year class matures. Alewife condition declined in 2025, which was expected given the relatively high Alewife density. Acoustic-based prey fish densities were greater than previous years acoustic estimates especially at depths from 180 – 220 m (591 – 722 ft), however acoustic based densities continue to be substantially lower than trawl-based densities. The 2025 biomass index was similar to 2024 for Emerald Shiner Notropis atherinoides and Threespine Stickleback Gasterosteus aculeatus , but was lower for Rainbow Smelt, and higher for Cisco Coregonus artedi . Three purported Bloater Coregonus hoyi were caught in the 2025 survey. Analysis of archived tissue identified five Bloater captured in previous surveys which increased the total number caught in Lake Ontario bottom trawl surveys to n = 24, since restoration stocking began in 2012. Whole lake density estimates of Lake Whitefish Coregonus clupeaformis increased in 2025 relative to 2024. Those density increases were due to increased catches in Canadian waters, as density in U.S. waters has remained low. The density index for wild or naturally reproduced juvenile Lake Trout Salvelinus namaycush increased in 2025 relative to 2024, with the most frequent catches occurring in waters around the Niagara River.

Lake Ontario↗
USGS2024

Origin of the Laurentian Great Lakes fish fauna through upward adaptive radiation cascade prior to the Last Glacial Maximum

The evolutionary histories of adaptive radiations can be marked by dramatic demographic fluctuations. However, the demographic histories of ecologically-linked co-diversifying lineages remain understudied. The Laurentian Great Lakes provide a unique system of two such radiations that are dispersed across depth gradients with a predator-prey relationship. We show that the North American Coregonus species complex (“ciscoes”) radiated rapidly prior to the Last Glacial Maximum (80–90 kya), a globally warm period, followed by rapid expansion in population size. Similar patterns of demographic expansion were observed in the predator species, Lake Charr ( Salvelinus namaycush ), following a brief time lag, which we hypothesize was driven by predator-prey dynamics. Diversification of prey into deep water created ecological opportunities for the predators, facilitating their demographic expansion, which is consistent with an upward adaptive radiation cascade. This study provides a new timeline and environmental context for the origin of the Laurentian Great Lakes fish fauna, and firmly establishes this system as drivers of ecological diversification and rapid speciation through cyclical glaciation.

Communications Biology↗
USGS2024

Factors influencing larval coregonine spatial distribution in Lake Geneva (Europe) and Lake Superior (North America) during a single season near known spawning sites

Survival rate of the larval stage is an important driver of fish recruitment. To understand mechanisms regulating larval survival it is important to understand the relative importance of abiotic and biotic factors that shape larval spatial distributions. We studied larval Coregonus distributions in surface waters (surface to 1 m) by repeatedly sampling study sites in two lakes that varied greatly in trophic state and regional climate. We evaluated the importance of bathymetric depth, Julian Day, edible zooplankton densities (EZ, ind. L −1 ) and wind vectors on larval spatial distributions using generalized additive modeling. In both systems, larval counts declined in a negative exponential fashion with bathymetric depth, indicating shallow depths are critical nursery habitat. The north-south wind vectors and Julian Day (which was positively correlated with surface temperature) influenced larval distributions in Lake Geneva with larval counts related to both variables linearly, whereas the east-west wind vector and EZ were unimportant. Highest larval counts were during an offshore south wind and declined slightly with Julian Day. In Lake Superior, bathymetric depth and the east-west wind vector influenced larval distributions and were unrelated to EZ, Julian Day, and the north-south wind vector. Larval counts were highest when onshore southwest winds preceded sampling. Differences in how wind affected larval distribution (offshore vs. onshore) might be related to larval size with Lake Superior larvae considerably smaller (average length 12.9 mm vs. 15.9 mm); thus, more apt to be subjected to advection. Within coastal waters, Julian Day and wind vectors influence distributions, but their importance seemingly varies lake-to-lake.

Minnesota↗
USGS2024

Larval coregonine density and diet composition along beaches of northern Lake Michigan

Recent oligotrophication in Lake Michigan has contributed to reduced biomass of spring zooplankton and a shift in the zooplankton assemblage toward more calanoid copepods. These changes have likely altered prey availability for first feeding native fish species that hatch in early spring, including coregonines. While spring zooplankton density and community composition are routinely monitored in offshore areas of Lake Michigan, descriptions of zooplankton in nearshore areas such as shallow beach environments and associated diet characteristics among larval coregonine species are limited. In this study, we describe the nearshore (<1 m depth, beach environment) zooplankton community in northeastern Lake Michigan during early spring 2015-2019 and compare the diets and diet selectivity of larval Lake Whitefish ( Coregonus clupeaformis ) and Cisco ( C. artedi ). Zooplankton density and composition varied among years, but calanoid copepods and copepod nauplii consistently dominated the zooplankton assemblage. Cisco and Lake Whitefish larvae were captured regularly, with Elk Rapids containing the highest proportion of Ciscoes each year. Calanoid and cyclopoid copepods were common in diets and estimated to have a positive selection. Although previous research has indicated high consumption of cyclopoid copepods by larval coregonines in Lake Michigan, our results provide new evidence that larval Lake Whitefish and Cisco of northeastern Lake Michigan will also consume and positively select for calanoid copepods when they are abundant. As such, should calanoid zooplankton continue to dominate the copepod community in Lake Michigan, larval coregonines appear capable of exploiting this abundant prey to improve their likelihood of survival to later life stages.

Michigan↗
USGS2024

Declines and shifts in morphological diversity of ciscoes (Coregonus spp.) in lakes Huron and Michigan, 1917–2019

Ciscoes ( Coregonus spp . ) were historically abundant and ecologically important in Laurentian Great Lakes ecosystems. Despite well-documented declines in their abundance and taxonomic diversity, declines in morphological diversity remain understudied. This knowledge gap is especially pertinent for lakes Michigan and Huron, which have each lost six of eight historical species. Improved understanding of historical and contemporary morphological diversity of Great Lakes ciscoes can inform ongoing restoration efforts and further elucidate the factors that contributed to declines. Our goal was to characterize shifts in morphological diversity of ciscoes in lakes Michigan and Huron over a century (1917–2019). We analyzed size-corrected morphometric and meristic measurements from three periods: Early (1917–1923), Middle (1950–1972), and Contemporary (2015–2019). We then identified morphologically distinct clusters while remaining agnostic to species identifications. We found that morphological diversity and the number of distinct clusters declined over time. We then leveraged species identifications to highlight key species losses and examine morphological shifts among extant species. Our findings provide insights into the historical and contemporary morphological diversity of ciscoes and will inform restoration efforts.

Lake Huron, Lake Michigan↗
USGS2023

Dispersive currents explain patterns of population connectivity in an ecologically and economically important fish

How to identify the drivers of population connectivity remains a fundamental question in ecology and evolution. Answering this question can be challenging in aquatic environments where dynamic lake and ocean currents coupled with high levels of dispersal and gene flow can decrease the utility of modern population genetic tools. To address this challenge, we used RAD-Seq to genotype 959 yellow perch ( Perca flavescens ), a species with an ~40-day pelagic larval duration (PLD), collected from 20 sites circumscribing Lake Michigan. We also developed a novel, integrative approach that couples detailed biophysical models with eco-genetic agent-based models to generate “predictive” values of genetic differentiation. By comparing predictive and empirical values of genetic differentiation, we estimated the relative contributions for known drivers of population connectivity (e.g., currents, behavior, PLD). For the main basin populations (i.e., the largest contiguous portion of the lake), we found that high gene flow led to low overall levels of genetic differentiation among populations ( F ST = 0.003). By far the best predictors of genetic differentiation were connectivity matrices that were derived from periods of time when there were strong and highly dispersive currents. Thus, these highly dispersive currents are driving the patterns of population connectivity in the main basin. We also found that populations from the northern and southern main basin are slightly divergent from one another, while those from Green Bay and the main basin are highly divergent ( F ST = 0.11). By integrating biophysical and eco-genetic models with genome-wide data, we illustrate that the drivers of population connectivity can be identified in high gene flow systems.

Lake Michigan↗
USGS2023

Larval cisco and lake whitefish exhibit high distributional overlap within nursery areas

Coregonine fishes, including lake whitefish ( Coregonus clupeaformis ) and cisco ( C. artedi ), are socioecologically important in the Laurentian Great Lakes and of conservation concern, but the processes driving recruitment variability are unclear. In Lake Ontario, cisco and lake whitefish exhibit similar spawning behaviours and early life histories, but population trajectories are diverging. One hypothesis is that sympatric cisco and lake whitefish larvae occupy distinct habitats and experience dissimilar local environmental conditions, despite co-occurrence within nursery areas. We described the spatiotemporal distributions of larval cisco and lake whitefish among multiple Lake Ontario embayment nursery areas, characterised physical habitat features associated with their distributions, determined the degree of spatial habitat partitioning between species and evaluated how habitat niche divergence occurred along an ontogenetic progression. Both species were widely distributed across larval nursery areas, though lake whitefish were less abundant and more narrowly distributed than cisco. Within the yolk sac stage, lake whitefish occupied more nearshore, shallower and colder waters than cisco, indicating potential habitat niche partitioning between congeners. However, distributional differences were subtle and likely driven by differential hatch timing and staggered ontogenetic habitat shifts. Combined, our results illustrate similar habitat use between cisco and lake whitefish through the larval stage and demonstrate that ontogeny and species-specific phenology influence habitat use for these species. This study provides additional evidence that the early life histories of cisco and lake whitefish are highly similar and does not support the hypothesis that larval habitat use differences are a major driver of differential recruitment success for these species.

New York↗
USGS2023

A science and management partnership to restore coregonine diversity to the Laurentian Great Lakes

Similar to many freshwater ecosystems, the Laurentian Great Lakes of North America have undergone numerous anthropogenic stressors resulting in considerable loss of biodiversity and habitat. Among Great Lakes fishes, the coregonine sub-family has endured the most extensive declines, including extinction of several species ( Coregonus johannae, C. alpenae , and C. kiyi orientalis ) and at least 10 instances of local extirpations of other species ( C. nigripinnis, C. reighardi, C. zenithicus, C. hoyi , and C. artedi ) across all 5 lakes, much of which occurred prior to the 1960s owing to overfishing, interactions with non-indigenous species, and habitat loss. Despite these declines, no federal-, provincial-, or state-mandated actions were ever implemented to conserve coregonine diversity, potentially because so much of the coregonine declines occurred prior to the enactment of federal conservation legislation. Possible explanations for inaction since enactment of that legislation include insufficient data on biological vulnerability or threats, unresolved taxonomy, and limited support from the fishery management agencies and their stakeholders prior to the 2000s. In recent decades, however, several fishery management agencies have undertaken efforts to re-introduce coregonine diversity. These efforts helped lead to development of a science-based framework to restore coregonines that was universally endorsed by fishery managers representing eight U.S. states, four U.S. tribal organizations, and the province of ON, Canada, in May 2018. The basin-wide framework is based on principles of conservation biology and adaptive management. We describe details of its key steps, including planning, restoring, and evaluating, while also describing recent implementation efforts to develop methods, improve available resources, and enhance coordination across the basin. Although our paper describes a regional effort to restore native coregonines, our adaptive-management approach could be used by other multi-agency stakeholders seeking to conserve or restore native fishes.

Laurentian Great Lakes↗
USGS2022

Lake Superior Kiyi reproductive biology

Objective The Lake Superior Kiyi Coregonus kiyi is an understudied species being considered for reintroduction into Laurentian Great Lakes where it no longer occurs. Herein, we provide descriptions of Kiyi reproductive biology with the intention of guiding potential gamete collections for propagation. Methods Data were collected on Kiyi spawning timing, spawning locations, spawning season catch rates, length at sexual maturity, sex ratios, fecundity, egg size, and larval occurrences in Lake Superior from 1996–2021. These data were compared to observations made a century prior in Lakes Michigan, Ontario, and Superior. Result Contemporary Kiyi spawning occurred between late December and late January when surface water temperatures cooled to <4°C. Spawning Kiyi were caught almost exclusively in 38.1-mm stretch mesh, as compared to larger meshes (50.8–76.2 mm). Capture depths for developing, ripe, running, and spent female Kiyi were similar and ranged from 82 to 221 m. Fifty percent of female and male Kiyi were classified as sexually mature at ~150 mm total length. Fecundity estimates ranged from 1,578 to 6,720 eggs/female. Mean diameter of unfertilized eggs was 1.7 mm. Recently hatched larval Kiyi were collected at the surface during May–July at 62 of the 113 locations sampled throughout the lake in 2019. Conclusion Our work suggests that Kiyi gamete collection efforts from mid-December through January using 38.1-mm gill-net panels set at bathymetric depths of at least 100 m would maximize the collection of spawning Kiyi and reduce the bycatch of other Coregonus species. Future research questions include the following: (1) “Do Kiyi form spawning aggregations at specific spawning areas, or do they spawn indiscriminately across the lake?”; (2) “Do Kiyi spawn near the bottom or up in the water column?”; (3) “What is the relationship between fall lake overturn and Kiyi spawn timing?”; and (4) “Could summer larval and age-0 Kiyi collections provide an opportunity for establishing a captive broodstock?”

Lake Superior↗