Variation in among‐family transcriptional responses to different environmental conditions can help to identify adaptive genetic variation, even prior to a selective event. Coupling differential gene expression with formal survival analyses allows for the disentanglement of treatment effects, required for understanding how individuals plastically respond to environmental stressors, from the adaptive genetic variation responsible for differential survival. We combined these two approaches to investigate responses to an emerging conservation issue, thiamine (vitamin B₁) deficiency, in a threatened population of Atlantic salmon (Salmo salar). Thiamine is an essential vitamin that is increasingly limited in many ecosystems. In Lake Champlain, Atlantic salmon cannot acquire thiamine in sufficient quantities to support natural reproduction; fertilized eggs must be reared in hatcheries and treated with supplemental thiamine. We evaluated transcriptional responses (via RNA sequencing) to thiamine treatment across families and found 3,616 genes differentially expressed between control (no supplemental thiamine) and treatment individuals. Fewer genes changed expression equally across families (i.e., additively) than exhibited genotype × environment interactions in response to thiamine. Differentially expressed genes were related to known physiological effects of thiamine deficiency, including oxidative stress, cardiovascular irregularities and neurological abnormalities. We also identified 1,446 putatively adaptive genes that were strongly associated with among‐family survival in the absence of thiamine treatment, many of which related to neurogenesis and visual perception. Our results highlight the utility of coupling RNA sequencing with formal survival analyses to identify candidate genes that underlie the among‐family variation in survival required for an adaptive response to natural selection.

Our study is the first comprehensive, multi-year assessment of polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), organochlorine pesticides (OCPs), polychlorinated naphthalenes (PCNs), polychlorinated dibenzo-p-dioxins, and polychlorinated dibenzofurans (PCDD/Fs) lake trout concentrations and trends in Lake Champlain (LC). Lake trout whole-fish, fillets, and eggs were collected over the 2012–2018 study period. Total PCB concentrations (395.7 ng/g wet weight (ww)) were the highest average concentration of any contaminant grouping reported in this study. Whole-fish lake trout modeling revealed highly significant (p < 0.05) log-linear correlations for all dioxin-like contaminants measured. Overall contaminant decreases for the 2012–2018 period ranged from 20.9% (total PCNs) to 39.3% (2378-TCDD). Contaminant decreases for total PCBs and total-5-PBDEs were 30.9% and 48.3%, respectively. Of particular significance were the measured total PBDE concentrations (74.3 ng/g ww) found in LC whole-fish lake trout. Log-linear forecasting indicates that whole-fish lake trout TEQs will be below the guidelines protective of wildlife thresholds during the periods 2035–2047 (TRGbird) and 2062–2088 (TRGmammal). Based on current USEPA guidelines, all lake trout fillets from Lake Champlain analyzed for this study exceed the human health cancer screening value of 0.15 pg-TEQ/g ww by a substantial margin (average = 8.61 pg-TEQ/g ww). Dioxin-like trend data collected for Lake Champlain indicates that the mechanisms of contaminant uptake, trends, and yearly percent decline reflect those found in the Great Lakes.

Runoff from two study watersheds in a cornfield in Charlotte, Vermont was monitored between October 1, 2015 and April 22, 2019 to evaluate the effects of construction in September 2017 of a grassed waterway in one of the watersheds. Flow rate and water quality data were obtained from 51 runoff events prior to construction of the grassed waterway and from 41 events following construction.

For each runoff event, data were aggregated to calculate total flow and runoff depth, mean concentrations of several fractions of phosphorus and nitrogen as well as chloride and total suspended solids, and total mass loads for the same monitored constituents. Total mass loads of constituents transported from the study watersheds during each runoff event were divided by the areas of the watersheds to calculate areal loads (mass per unit area) to facilitate comparison with data from other Vermont fields. All data were log10 transformed to meet the assumptions of parametric statistical tests.

Constituent concentrations and loads recorded at the Charlotte study watersheds were generally within the range observed at the other Vermont edge-of-field monitoring sites between 2013 – 2019 (Stone Environmental, 2016), with a few exceptions. Areal loads of total suspended solids from both Charlotte study watersheds were substantially higher than those recorded at the other monitored fields. Mean chloride concentrations from the Charlotte watersheds were at the very high end of the range observed across all the other monitored fields and areal chloride loads were substantially higher than those observed at other monitored fields.

Mercury and cyanotoxins in Lake Champlain pose health concerns to humans and the ecosystem. Mercury poisoning through the consumption of contaminated fish has been well documented for more than half a decade, typically with top predators posing the greatest threat. And while the most common route of cyanotoxin intoxication is exposure through drinking water and recreational contact, research has shown cyanotoxin levels in fish can reach concentrations that pose health risks, if consumed. The aim of this study was two-fold, 1) to reassess fish mercury throughout the lake to determine which species at what size pose a health concern, identify areas that are disproportionally impacted by mercury and assess long-term changes, along with 2) determining if cyanotoxins are present in fish, and if so, do concentrations in fish correlate with presence in water samples.

More than 600 fish of five species (smallmouth bass, walleye, lake trout, yellow perch and white perch) from the seven segments of Lake Champlain (South Lake, South Main Lake, Main Lake, North Main Lake, Malletts Bay, Northeast Arm and Missisquoi Bay) were analyzed for total mercury. While all fish species had specimens exceed the US EPA mercury advisory limit of 300 ppb, walleye and smallmouth bass had 38% (28/74) and 17% (27/157) of their specimens, respectively, exceed the USFDA action limit of 1000 ppb. Fish length and location were significant factors explaining mercury variability for the five species tested, however, no consistent trend was observed for location among species. Because these species include cold, cool and warm-water fish feeding from benthic and pelagic food webs along with different growth rates and efficiencies, utilizing fish mercury concentrations to determine lake segments that are disproportionately affected by mercury was inconclusive.

Assessing long-term mercury trends in fish shows a significant decrease in lake trout, walleye and yellow perch from their initial mercury surveys (1987-1990). Smallmouth bass and white perch did not show a significant decrease from their initial surveys in the mid-1990s. An unexpected finding was the increase in smallmouth bass and yellow perch mercury concentrations since the 2011 study. Similar findings have been documented in the Great Lakes region and Ontario with proposed explanations including enhanced deposition from Asia, invasive species and climate change. These along with impacts of Hurricane Irene in 2011 are plausible explanations for the increase in Lake Champlain fish mercury but require additional research.

Cyanotoxins (microcystins, anatoxin-a and cylindrospermopsin) were measured in water samples collected throughout the summer and fish samples during low and high bloom periods from the Main Lake and Missisquoi Bay. Analysis utilized HPLC coupled with tandem mass spectrometry able to detect microcystin metabolites, a technical advancement over ELISA that can react with non-microcystin metabolites leading to spuriously high values. However, all water and fish measurements were below the detection level agreeing with VT DEC data showing no microcystin or anatoxin in water samples during this time period. Although correlations of cyanotoxin concentrations between water and fish could not be compared due to non-detectable levels, the study validated the method used for microcystin detection and demonstrated microcystin, anatoxin and cylindrospermopsin did not bioaccumulate in fish as cyanotoxins were present in 2015.

Mercury concentrations in Lake Champlain fish increased (2011–2017) for the first time in more than two decades. The increase, however, was not consistent among species or throughout the lake. Mercury concentrations in smallmouth bass and yellow perch from the three Main Lake segments increased significantly while concentrations in the eastern portions of the lake (Northeast Arm and Malletts Bay) remained unchanged or decreased; mercury concentrations in white perch remained unchanged. Factors examined to explain the increase included: atmospheric deposition, lake temperature, chlorophyll-a, fishery dynamics, lake flooding and loading of total suspended solids (TSS). This paper examines how each factor has changed between study periods and the spatial variability associated with the change. We hypothesize fishery dynamics, flooding and TSS loading may be partially responsible for the increase in fish mercury. Both growth efficiency and biomass of fish suggest mercury concentrations would increase in the Main Lake segments and decrease in the eastern portion of the lake. Additionally, two extreme climate events in 2011 resulted in extensive flooding and a four-fold increase in annual TSS loading, both potentially increasing biotic mercury with the impact varying spatially throughout the lake. Changes to the fishery and disturbance caused by extreme climatic events have increased biotic mercury and the processes responsible need further study to identify possible future scenarios in order to better protect human and wildlife health.