Response of fish assemblages to restoration of rapids habitat in a Great Lakes connecting channel

Rapids habitats are critical spawning and nursery grounds for multiple Laurentian Great Lakes fishes of ecological importance such as lake sturgeon, walleye, and salmonids. However, river modifications have destroyed important rapids habitat in connecting channels by modifying flow profiles and removing large quantities of cobble and gravel that are preferred spawning substrates of several fish species. The conversion of rapids habitat to slow moving waters has altered fish assemblages and decreased the spawning success of lithophilic species. The St. Marys River is a Great Lakes connecting channel in which the majority of rapids habitat has been lost. However, rapids habitat was restored at the Little Rapids in 2016 to recover important spawning habitat in this river. During the restoration, flow and substrate were recovered to rapids habitat. We sampled the fish community (pre- and post-restoration), focusing on age-0 fishes in order to characterize the response of the fish assemblage to the restoration, particularly for species of importance (e.g. lake whitefish, walleye, Atlantic salmon). Following restoration, we observed a 40% increase in age-0 fish catch per unit effort, increased presence of rare species, and a shift in assemblage structure of age-0 fishes (higher relative abundance of Salmonidae, Cottidae, and Gasterosteidae). We also observed a “transition” period in 2017, in which the assemblage was markedly different from the pre- and post-restoration assemblages and was dominated by Catostomidae. Responses from target species were mixed, with increased Atlantic salmon abundance, first documented presence of walleye and no presence of lake sturgeon or Coregoninae.     

Asymmetric Hybridization of Pink (Oncorhynchus gorbuscha) and Chinook (O. tshawytscha) Salmon in the St. Marys River,Michigan

Natural hybridization between pink salmon (Oncorhynchus gorbuscha) and Chinook salmon (O. tshawytscha) has been observed only in the Great Lakes, where both species have been introduced. The direction of hybridization between these species is poorly understood, thus the present study analyzed mitochondrial DNA (mtDNA) to determine whether the maternal parents were pink or Chinook salmon. During annual salmon population surveys on the St. Marys River (1998–2002), fifty putative hybrids of pink salmon and Chinook salmon were identified from meristic, morphometric and color characters. We designed primers to amplify a fragment of the mitochondrial D-loop control region that included both a variable and a control restriction site (BstNI). Polymerase chain reaction, restriction endonuclease digestion and capillary electrophoresis of mtDNA were used in order to identify the maternal parent of each hybrid salmon. In addition, the amplified fragments from the three fish species were sequenced to further verify the results. All hybrid salmon specimens were found to possess Chinook salmon mtDNA, indicating that hybridization between Chinook salmon and pink salmon is asymmetrical and likely unidirectional, occurring only between male pink salmon and female Chinook salmon. Influences contributing to the hybridization of these salmonid species could include limited spatial and temporal segregation of spawners, sexual selection, a limiting number of Chinook males, and/or physiological factors.     

Implications of tagging effects for interpreting the performance of sea lamprey traps in a large river

Abundance estimates can be crucial for managing species of economic concern. The accuracy of these estimates can depend on the methods used to track animals and to estimate abundance from tracking data. We tested experimentally if disparate estimates of trapping efficiency calculated for sea lamprey (Petromyzon marinus) in the St. Marys River near Sault Ste. Marie, Canada could be explained by effects related to the invasiveness and handling involved in tagging or the tag size used in the marking procedures. Trapping is used to gauge adult abundance, trapping efficiency, and success of a binational sea lamprey control program in the Laurentian Great Lakes, North America. Our experiment compared nightly catches of sea lamprey marked with external fin clips, surgically-implanted passive integrated transponder tags (PIT-only), and surgically-implanted PIT and acoustic tags (PIT+acoustic). We found no evidence that the probability of being trapped was affected by the added invasiveness and handling of internal tagging. Nightly recaptures of PIT-only tagged sea lamprey, relative to fin-clipped sea lamprey, were not different from expectations based on the numbers of individuals released from each treatment group. Conversely, there was evidence of effects related to tag size. Nightly recaptures of PIT+acoustic tagged sea lamprey, relative to PIT-only tagged sea lamprey, were lower than expected based on numbers of individuals released from each treatment group. Effects related to tag size partially explain the disparate estimates in trapping efficiency observed for sea lamprey.     

Evidence of lake trout (Salvelinus namaycush) spawning and spawning habitat use in the Dog River,Lake Superior

Lake trout spawn primarily in lakes, and the few river-spawning populations that were known in Lake Superior were believed to be extirpated. We confirmed spawning by lake trout in the Dog River, Ontario, during 2013–2016 by the collection of and genetic identification of eggs, and we describe spawning meso- and microhabitat use by spawning fish. Between 2013 and 2016, a total of 277 lake trout eggs were collected from 39 of 137 sampling locations in the river. The majority of eggs (220) were collected at the transition between the estuary and the river channel crossing the beach. Lake trout eggs were most often located near the downstream end of pools in areas characterized by rapid changes in depth or slope, coarse substrates, and increased water velocities, where interstitial flows may occur. Depths in wadeable areas where eggs were found averaged 0.9?m (range: 0.4 to 1.3?m) and substrate sizes consisted of large gravel, cobble, and boulder; comparable to spawning characteristics noted in lakes. Water velocities averaged 0.66?m·s^?1 (range: 0.33 to 1.7?m³·s^?1) at mid-depth. This information on spawning habitat could be used to help locate other remnant river-spawning populations and to restore river-spawning lake trout and their habitat in rivers that previously supported lake trout in Lake Superior. The Dog River population offers a unique opportunity to understand the ecology of a river spawning lake trout population.     

Temporal and spatial trends of organochlorines and mercury in fishes from the St. Clair River/Lake St. Clair corridor,Canada

The temporal and spatial relationships of a suite of organochlorine contaminants and mercury were examined in various fish species of the St. Clair River/Lake St. Clair corridor, Canada, in order to evaluate the effectiveness of remediation efforts and to assess the risk to human and wildlife fish consumers. In Lake St. Clair, fish tissue concentrations of mercury, polychlorinated biphenyls (PCBs), octachlorostyrene (OCS), hexachlorobenzene (HCB), and dichlorodiphenyltrichloroethane (DDT) decreased consistently from the 1970s until the 1980s and 1990s, after which the rate of contaminant decline slowed or concentrations stabilized. This trend was consistent in up to 13 species (both young-of-the-year and adult fishes) comprising different trophic positions and dietary habits, suggesting that the changes were reflective of ambient conditions rather than food web processes. Elevated concentrations of mercury, PCBs, OCS, HCB, and DDT were detected in St. Clair River young-of-the-year spottail shiner compared with fish from Lake Huron, indicating that non-atmospheric inputs of these chemicals, likely originating from sediment, remain in the St. Clair River. Current concentrations of mercury and PCBs, and mercury, PCBs, and DDT remain of concern to human and wildlife fish consumers, respectively. Given that contaminant decreases have generally stabilized in fish, we suggest that further natural recovery of contaminants in St. Clair corridor fishes will be slow since contaminants will likely continue to be influenced by sediment levels.     

Establishment patterns of non-native fishes: Lessons from the Duluth-Superior harbor and lower St. Louis River, an invasion-prone Great Lakes coastal ecosystem

We conducted a 2-year, multi-gear survey in the lower St. Louis River, which includes the Duluth-Superior harbor, an international shipping port and non-native species invasion “hotspot.” Our objectives were to quantify the contribution of non-native species to the overall fish assemblage and assess their spatial distribution and abundance. We captured 10 non-native fishes; none, however, were first detections. Non-native fishes composed roughly one quarter of the total species richness, were found in 84% of samples, and composed 15% of the total abundance. The spatial distribution and abundance of non-native fishes was dependent on gear selection (and thereby habitat selection), sampling location, and abundance measure (individuals or biomass). We used a recently published non-native species establishment framework to integrate catch data from the different gears. Viewed in the context of this framework, we identified only two non-native fishes, Eurasian ruffe (Gymnocephalus cernuus) and round goby (Neogobius melanostomus), as both widespread and abundant, whereas we identified three as localized and rare. Moreover, the time since first detection of non-native fishes was not predictive of their frequency of occurrence across the study area, underscoring the importance of environmental and biological factors in controlling fish establishment success. Although non-native fishes constitute a considerable portion of the trawl catch in the river channel, from a multi-gear system-wide perspective, native fishes collectively make up the majority of the fish biomass and abundance in the lower St. Louis River.     

Recolonization of lake whitefish river spawning ecotypes and estimates of riverine larval production in Green Bay,Lake Michigan

Lake whitefish (Coregonus clupeaformis) within the waters of Green Bay, Lake Michigan have recently shown a substantial increase in abundance. Furthermore, after over 100 years of extirpation, adult lake whitefish are found spawning within major Wisconsin tributaries to Green Bay. Many knowledge gaps still exist with respect to the chronology of adult river migrations, including the physical characteristics of upstream habitats selected for reproduction and the extent of larval production by these riverine ecotypes. Here, we use hydroacoustic imaging along with egg and larval surveys to evaluate this novel riverine spawning in 2017 and 2018. Highest abundance of adults was observed in the month of November as temperatures declined below 8 °C. Spawning areas consisted of cobble substrates, and site-specific fish densities were primarily correlated with river flows between 0.3 and 1.0 m/s, with specific values varying by tributary and year. Locations of egg deposition mirrored areas of high observed fish densities. Larval production was documented on each tributary using active trawl ichthyoplankton sampling, and larvae were observed outmigrating to open water environments. We estimated tributaries produced 452,000 larvae in 2017 and 721,000 larvae in 2018. To our knowledge, this represents the first documentation of successful lake whitefish larval production from Green Bay tributaries and suggests tributary spawning populations contribute to the greater abundance of lake whitefish observed in recent years.     

Genetic assessment of straying rates of wild and hatchery reared lake sturgeon (Acipenser fulvescens) in Lake Superior tributaries

Natal philopatry in lake sturgeon (Acipenser fulvescens) has been hypothesized to be an important factor that has lead to genetically distinct Great Lakes populations. Due to declining abundance, population extirpation, and restricted distribution, hatchery supplementation is being used to augment natural recruitment and to reestablish populations. If hatchery-reared lake sturgeon are more likely to stray than naturally produced individuals, as documented in other well-studied species, outbreeding could potentially jeopardize beneficial site-specific phenotypic and genotypic adaptations. From 1983 to 1994, lake sturgeon propagated using eggs taken from Lake Winnebago adults (Lake Michigan basin) were released in the St. Louis River estuary in western Lake Superior. Our objective was to determine whether these introduced individuals have strayed into annual spawning runs in the Sturgeon River, Michigan. Additionally, we estimated a natural migration rate between the Sturgeon River and Bad River, Wisconsin populations. Presumed primiparous lake sturgeon sampled during Sturgeon River spawning runs from 2003 to 2008 were genotyped at 12 microsatellite loci. Genotypic baselines established for the Sturgeon River (n = 101), Bad River (n = 40), and Lake Winnebago river system (n = 73) revealed a relatively high level of genetic divergence among populations (mean F_ST = 0.103; mean R_ST = 0.124). Likelihood-based assignment tests indicated no straying of stocked Lake Winnebago strain lake sturgeon from the St. Louis River into the Sturgeon River spawning population. One presumed primiparous Sturgeon River individual likely originated from the Bad River population. Four first-generation migrants were detected in the Sturgeon River baseline, indicating an estimated 3.5% natural migration rate for the system.     

Molecular sexing of lake sturgeon

Demographic data including characterizations of population sex and age composition are of fundamental importance for effective management, especially for numerically depressed Great Lakes populations of imperiled species such as lake sturgeon (Acipenser fulvescens). The goal of this paper was to extend a recently reported Acipenserid-derived PCR-based genotyping test to determine sex of lake sturgeon. We demonstrate that the recently reported AllWSex2 primers amplified the female sex-specific region in lake sturgeon of known sex, consistent with a ZZ/ZW mode of inheritance. Sanger sequencing of female lake sturgeon PCR products matched published sequences from female sterlet (Acipenser ruthenus), showing 100% query cover and 98% (63/64) identity. The ability to provide a rapid, cost-effective, and unambiguous determination of sex for lake sturgeon will allow managers to determine compositional estimates of sex ratios during any season, and for individuals at any age or size, which is of great utility for species characterized by delayed sexual maturity and lacking external sexual dimorphisms.     

Predicting submerged aquatic vegetation cover and occurrence in a Lake Superior estuary

Submerged aquatic vegetation (SAV) provides the biophysical basis for multiple ecosystem services in Great Lakes estuaries. Understanding sources of variation in SAV is necessary for sustainable management of SAV habitat. From data collected using hydroacoustic survey methods, we created predictive models for SAV in the St. Louis River Estuary (SLRE) of western Lake Superior. The dominant SAV species in most areas of the estuary was American wild celery (Vallisneria americana Michx.). Maximum depth of SAV in 2011 was approximately 2.1 m. In regression tree models, most of the variation in SAV cover was explained by an autoregression (lag) term, depth, and a measure of exposure based on fetch. Logistic SAV occurrence models including water depth, exposure, bed slope, substrate fractal dimension, lag term, and interactions predicted the occurrence of SAV in three areas of the St. Louis River with 78–86% accuracy based on cross validation of a holdout dataset. Reduced models, excluding fractal dimension and the lag term, predicted SAV occurrence with 75–82% accuracy based on cross validation and with 68–85% accuracy for an independent SAV dataset collected using a different sampling method. In one area of the estuary, the probability of SAV occurrence was related to the interaction of depth and exposure. At more exposed sites, SAV was more likely to occur in shallow areas than at less exposed sites. Our predictive models show the range of depth, exposure, and bed slope favorable for SAV in the SLRE; information useful for planning shallow-water habitat restoration projects.     

St. Clair-Detroit River system: Phosphorus mass balance and implications for Lake Erie load reduction,monitoring, and climate change

To support the 2012 Great Lakes Water Quality Agreement on reducing Lake Erie's phosphorus inputs, we integrated US and Canadian data to update and extend total phosphorus (TP) loads into and out of the St. Clair-Detroit River System for 1998–2016. The most significant changes were decreased loads from Lake Huron caused by mussel-induced oligotrophication of the lake, and decreased loads from upgraded Great Lakes Water Authority sewage treatment facilities in Detroit. By comparing Lake St. Clair inputs and outputs, we demonstrated that on average the lake retains 20% of its TP inputs. We also identified for the first time that loads from resuspended Lake Huron sediment were likely not always detected in US and Canadian monitoring programs due to mismatches in sampling and resuspension event frequencies, substantially underestimating the load. This additional load increased over time due to climate-induced decreases in Lake Huron ice cover and increases in winter storm frequencies. Given this more complete load inventory, we estimated that to reach a 40% reduction in the Detroit River TP load to Lake Erie, accounting for the missed load, point and non-point sources other than that coming from Lake Huron and the atmosphere would have to be reduced by at least 50%. We also discuss the implications of discontinuous monitoring efforts.     

Application of distance sampling techniques for diving ducks on Lake St. Clair and western Lake Erie

Lake St. Clair and western Lake Erie are important migration staging areas for diving ducks including canvasbacks (Aythya valisineria), redheads (Aythya americana), and lesser and greater scaup (Aythya affinis and Aythya marila). Starting in 1983, the Michigan Department of Natural Resources (MDNR) attempted to census diving ducks on the United States portion of Lake St. Clair throughout autumn migration; however, in 2010 the MDNR expanded the traditionally surveyed area to include all of Lake St. Clair and a portion of western Lake Erie. The idea of achieving a census over the expanded study area was unrealistic, and instead distance sampling techniques were adopted in an effort to generate statistically valid estimates of detection probabilities and abundances for diving ducks during spring and autumn migration. We found distance sampling techniques to be a viable option for estimating diving duck abundance as long as flock size is accounted for as a covariate affecting the detection function. Diving ducks were generally more abundant on our study area during autumn migration with a mean of 306,327 ducks/survey (SE = 40,729) compared to an average spring abundance of 91,053 ducks/survey (SE = 19,175). Peak abundance occurred on 20 November 2012 with an estimated 596,335 diving ducks on Lake St. Clair and western Lake Erie. Ultimately, our methodology could be used to establish long-term, standardized data collection techniques and applied to conservation planning for waterfowl in the Great Lakes region.     

Bed morphology, flow structure, and sediment transport at the outlet of Lake Huron and in the upper St. Clair River

An integrated multibeam echo sounder and acoustic Doppler current profiler field survey was conducted in July 2008 to investigate the morphodynamics of the St. Clair River at the outlet of Lake Huron. The principal morphological features of the upper St. Clair River included flow-transverse bedforms that appear weakly mobile, erosive bedforms in cohesive muds, thin non-cohesive veneers of weakly mobile sediment that cover an underlying cohesive (till or glacio-lacustrine) surface, and vegetation that covers the bed. The flow was characterized by acceleration as the banks constrict from Lake Huron into the St. Clair River, an approximately 1500-m long region of flow separation downstream from the Blue Water Bridge, and secondary flow connected to: i) channel curvature; ii) forcing of the flow by local bed topography, and iii) flow wakes in the lee side of ship wrecks. Nearshore, sand-sized, sediment from Lake Huron was capable of being transported into, and principally along, the banks of the upper St. Clair River by the measured flow. A comparison of bathymetric surveys conducted in 2007 and 2008 identifies that the gravel bed does undergo slow downstream movement, but that this movement does not appear to be generated by the mean flow, and could possibly be caused by ship-propeller-induced turbulence. The study results suggest that the measured mean flow and dredging within the channel have not produced major scour of the upper St. Clair River and that the recent fall in the level of Lake Huron is unlikely to have been caused by these mechanisms.