A novel approach to assessing natural resource injury with Bayesian networks.

Quantifying the effects of environmental stressors on natural resources is problematic because of complex interactions among environmental factors that influence endpoints of interest. This complexity, coupled with data limitations, propagates uncertainty that can make it difficult to causally associate specific environmental stressors with injury endpoints. The Natural Resource Damage Assessment and Restoration (NRDAR) regulations under the Comprehensive Environmental Response, Compensation, and Liability Act and Oil Pollution Act aim to restore natural resources injured by oil spills and hazardous substances released into the environment; exploration of alternative statistical methods to evaluate effects could help address NRDAR legal claims. Bayesian networks (BNs) are statistical tools that can be used to estimate the influence and interrelatedness of abiotic and biotic environmental variables on environmental endpoints of interest. We investigated the application of a BN for injury assessment using a hypothetical case study by simulating data of acid mine drainage (AMD) affecting a fictional stream-dwelling bird species. We compared the BN-generated probability estimates for injury with a more traditional approach using toxicity thresholds for water and sediment chemistry. Bayesian networks offered several distinct advantages over traditional approaches, including formalizing the use of expert knowledge, probabilistic estimates of injury using intermediate direct and indirect effects, and the incorporation of a more nuanced and ecologically relevant representation of effects. Given the potential that BNs have for natural resource injury assessment, more research and field-based application are needed to determine their efficacy in NRDAR. We expect the resulting methods will be of interest to many US federal, state, and tribal programs devoted to the evaluation, mitigation, remediation, and/or restoration of natural resources injured by releases or spills of contaminants. Integr Environ Assess Manag 2024;20:562-573. Published 2023. This article is a U.S. Government work and is in the public domain in the USA. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Evolutionary and ecological correlates of thiaminase in fishes.

Thiamine (vitamin B1) is required by all living organisms in multiple metabolic pathways. It is scarce in natural systems, and deficiency can lead to reproductive failure, neurological issues, and death. One major cause of thiamine deficiency is an overreliance on diet items containing the enzyme thiaminase. Thiaminase activity has been noted in many prey fishes and linked to cohort failure in salmonid predators that eat prey fish with thiaminase activity, yet it is generally unknown whether evolutionary history, fish traits, and/or environmental conditions lead to production of thiaminase. We conducted literature and GenBank BLAST sequence searches to collect thiaminase activity data and sequence homology data in expressed protein sequences for 300 freshwater and marine fishes. We then tested whether presence or absence of thiaminase could be predicted by evolutionary relationships, trophic level, omega-3 fatty acid concentrations, habitat, climate, invasive potential, and body size. There was no evolutionary relationship with thiaminase activity. It first appears in Class Actinoptergyii (bony ray-finned fishes) and is present across the entire Actinoptergyii phylogeny in both primitive and derived fish orders. Instead, ecological factors explained the most variation in thiaminase: fishes were more likely to express thiaminase if they fed closer to the base of the food web, were high in polyunsaturated fatty acids, lived in freshwater, and were from tropical climates. These data provide a foundation for understanding sources of thiaminase leading to thiamine deficiency in fisheries and other organisms, including humans that eat uncooked fish.

Overemphasis on publications may disadvantage historically excluded groups in STEM before and during COVID-19: A North American survey-based study.

Publishing is a strong determinant of academic success and there is compelling evidence that identity may influence the academic writing experience and writing output. However, studies rarely quantitatively assess the effects of major life upheavals on trainee writing. The COVID-19 pandemic introduced unprecedented life disruptions that may have disproportionately impacted different demographics of trainees. We analyzed anonymous survey responses from 342 North American environmental biology graduate students and postdoctoral scholars (hereafter trainees) about scientific writing experiences to assess: (1) how identity interacts with scholarly publication totals and (2) how the COVID-19 pandemic influenced trainee perceptions of scholarly writing productivity and whether there were differences among identities. Interestingly, identity had a strong influence on publication totals, but it differed by career stage with graduate students and postdoctoral scholars often having opposite results. We found that trainees identifying as female and those with chronic health conditions or disabilities lag in publication output at some point during training. Additionally, although trainees felt they had more time during the pandemic to write, they reported less productivity and motivation. Trainees who identified as female; Black, Indigenous, or as a Person of Color [BIPOC]; and as first-generation college graduates were much more likely to indicate that the pandemic affected their writing. Disparities in the pandemic's impact on writing were most pronounced for BIPOC respondents; a striking 85% of BIPOC trainees reported that the pandemic affected their writing habits, and overwhelmingly felt unproductive and unmotivated to write. Our results suggest that the disproportionate impact of the pandemic on writing output may only heighten the negative effects commonly reported amongst historically excluded trainees. Based on our findings, we encourage the academy to consider how an overemphasis on publication output during hiring may affect historically excluded groups in STEM-especially in a post-COVID-19 era.

Thiamine Supplementation Improves Survival and Body Condition of Hatchery-Reared Steelhead (Oncorhynchus mykiss) in Oregon.

Early rearing of steelhead (Oncorhynchus mykiss) in Oregon hatcheries is often problematic; fry can become emaciated and die during the period between hatch and first feed. Thiamine (vitamin B1) deficiency has caused early mortality in salmonids; however, the thiamine status of Oregon's steelhead populations is unknown, to date. Of the 26 egg samples from three Oregon hatcheries in 2019, 20 (77%) had thiamine levels < 10 nmol/g, and 13 of those samples (50%) had levels <6.5 nmol/g, suggesting the thiamine deficiency of adult, female steelhead. To investigate if thiamine deficiency was causally related to fry survival, females were injected with buffered thiamine HCl 50 mg/kg prior to spawning; additionally, a subset of eggs were supplemented via bath treatment with thiamine mononitrate (1000 ppm) at spawning. Cumulative fry mortality at 8 weeks post-hatch from thiamine-injected females was 2.9% compared to 13.8% mortality of fry without thiamine supplementation. Fry treated only with the thiamine via bath as eggs had a mortality rate of 6.9%. There were no additional improvements for the survival of fry from injected females that also received a thiamine bath. Furthermore, condition factors were greater in thiamine-supplemented fry than in those that received no thiamine. These data identify thiamine deficiency in Oregon steelhead and suggest supplementation with thiamine can mitigate early rearing mortality.

Complex Life Histories Alter Patterns of Mercury Exposure and Accumulation in a Pond-Breeding Amphibian.

Quantifying how contaminants change across life cycles of species that undergo metamorphosis is critical to assessing organismal risk, particularly for consumers. Pond-breeding amphibians can dominate aquatic animal biomass as larvae and are terrestrial prey as juveniles and adults. Thus, amphibians can be vectors of mercury exposure in both aquatic and terrestrial food webs. However, it is still unclear how mercury concentrations are affected by exogenous (e.g., habitat or diet) vs endogenous factors (e.g., catabolism during hibernation) as amphibians undergo large diet shifts and periods of fasting during ontogeny. We measured total mercury (THg), methylmercury (MeHg), and isotopic compositions (δ 13C, δ15N) in boreal chorus frogs (Pseudacris maculata) across five life stages in two Colorado (USA) metapopulations. We found large differences in concentrations and percent MeHg (of THg) among life stages. Frog MeHg concentrations peaked during metamorphosis and hibernation coinciding with the most energetically demanding life cycle stages. Indeed, life history transitions involving periods of fasting coupled with high metabolic demands led to large increases in mercury concentrations. The endogenous processes of metamorphosis and hibernation resulted in MeHg bioamplification, thus decoupling it from the light isotopic proxies of diet and trophic position. These step changes are not often considered in conventional expectations of how MeHg concentrations within organisms are assessed.

Asynchrony, density dependence, and persistence in an amphibian.

Understanding drivers of metapopulation dynamics remains a critical challenge for ecology and conservation. In particular, the degree of synchrony in metapopulation dynamics determines how resilient a metapopulation is to a widespread disturbance. In this study, we used 21 years of egg mass count data across 64 nonpermanent freshwater ponds in Connecticut, USA to evaluate patterns of abundance and growth and to assess regional as well as local factors in shaping the population dynamics of wood frogs (Rana sylvatica = Lithobates sylvaticus). In particular, we asked whether a species known to undergo metapopulation dynamics exhibited spatial synchrony in abundances. With the exception of a single year when breeding took place during severe drought conditions, our analyses revealed no evidence of synchrony despite close proximity (mean minimum distance < 300 m) of breeding ponds across the 3213-ha study area. Instead, local, pond-scale conditions best predicted patterns of abundance and population growth rate. We found negative density dependence on population growth rate within ponds as well as evidence that larger neighboring pond populations had a negative effect on focal ponds. Beyond density, pond depth was a critical predictor; deeper ponds supported larger populations. Drought conditions and warm winters negatively affected populations. Overall, breeding ponds vary in critical ways that either support larger, more persistent populations or smaller populations that are not represented by breeding pairs in some years. The infrequency of spatial synchrony in this system is surprising and suggests greater resilience to stressors than would have been expected if dynamics were strongly synchronized. More generally, understanding the characteristics of systems that determine synchronous population dynamics will be critical to predicting which species are more or less resilient to widespread disturbances like land conversion or climate change.

Direct effects influence larval salamander size and density more than indirect effects.

Direct and indirect effects both influence population and community dynamics. The relative strengths of these pathways are often compared using experimental approaches, but their evaluation in situ has been less frequent. We examined how individual and aggregate impacts of direct and indirect effects of species densities, proxies for competition and predation pressure, and habitat variables influenced patterns of larval density and body size of ringed (Ambystoma annulatum) and spotted salamanders (A. maculatum). We surveyed > 150 ponds in Missouri, USA, from 2012 to 2014 to measure the density and body size of each focal species, the density of co-occurring pond food web members, and select habitat features. We used structural equation modeling to quantify the relative importance of direct and indirect pathways on both body size and larval density. Overall, both responses were explained through a combination of direct and indirect effects. However, the magnitudes of direct effects were often greater than indirect effects. Some of the direct and indirect relationships with larval salamander size and density were also consistent with results from experimental studies. Finally, total direct and indirect effects were often weaker due to habitat and density variables negating each other's impacts. Overall, our study shows that direct effects were equivalent to, or more important than, indirect effects. We also demonstrate that the effects stemming from individual relationships can sum to produce net patterns that are negligible in magnitude. Further work on direct and indirect effects with observational data are needed to examine their magnitudes in natural communities.

Recent Patterns in Lake Erie Phosphorus and Chlorophyll a Concentrations in Response to Changing Loads.

Despite the initial success of extensive efforts to reduce phosphorus (P) loading to Lake Erie as a part of the Great Lakes Water Quality Agreement, Lake Erie appears to be undergoing a re-eutrophication and it is plagued by harmful algal blooms. To offer insights into potential lake responses under differing Maumee River loads and reveal recent changes with time, we explored patterns in phosphorus and chlorophyll a data from 2008 to 2018 collected in western Lake Erie near the mouth of the Maumee River. We found high, but relatively stable Maumee River and lake concentrations of total P (TP) and soluble reactive P (SRP) with no discernable annual or seasonal patterns. Maumee spring TP load was not strongly related to lake TP, and lake SRP concentrations were positively but weakly related to SRP loads. Lake TP was a strong predictor of chlorophyll a, but the relationship was weaker at sites closer to the Maumee. These results highlight spatial differences both in P concentration and the relationship between TP and chlorophyll a, and these indicate that spring phosphorus loads are a weak algal biomass predictor in the portion of the western basin of Lake Erie represented by these sampling stations.

Effects of the Neonicotinoid Insecticide Clothianidin on Southern Leopard Frog (Rana sphenocephala) Tadpole Behavior.

Neonicotinoid insecticides are highly water soluble with relatively long half-lives, which allows them to move into and persist in aquatic ecosystems. However, little is known of the impacts of neonicotinoids on non-target vertebrates, especially at sublethal concentrations. We evaluated the effects of the neonicotinoid clothianidin on the behavior of southern leopard frog tadpoles (Rana sphenocephala) after a 96-h exposure at 6 concentrations, including 0 (control), 0.375, 0.75, 1.5, 3.0, 6.0 µg/L. We quantified total displacement, mean velocity, maximum velocity, and time spent moving of tadpoles for 1 h post-exposure. Total displacement and mean velocity of tadpoles decreased with clothianidin exposure. Maximum velocity decreased linearly with concentration, but there was no relationship between time spent moving and clothianidin concentration. Our results suggest exposure to clothianidin at sublethal concentrations can affect movement behavior of non-target organisms such as tadpoles.

Variation in phenology and density differentially affects predator-prey interactions between salamanders.

Variation in the timing of breeding (i.e., phenological variation) can affect species interactions and community structure, in part by shifting body size differences between species. Body size differences can be further altered by density-dependent competition, though synergistic effects of density and phenology on species interactions are rarely evaluated. We tested how field-realistic variation in phenology and density affected ringed salamander (Ambystoma annulatum) predation on spotted salamanders (Ambystoma maculatum), and whether these altered salamander dynamics resulted in trophic cascades. In outdoor mesocosms, we experimentally manipulated ringed salamander density (low/high) and breeding phenology (early/late) of both species. Ringed salamander body size at metamorphosis, development, and growth were reduced at higher densities, while delayed phenology increased hatchling size and larval development, but reduced relative growth rates. Survival of ringed salamanders was affected by the interactive effects of phenology and density. In contrast, spotted salamander growth, size at metamorphosis, and survival, as well as the biomass of lower trophic levels, were negatively affected primarily by ringed salamander density. In an additional mesocosm experiment, we isolated whether ringed salamanders could deplete shared resources prior to their interactions with spotted salamanders, but instead found direct interactions (e.g., predation) were the more likely mechanism by which ringed salamanders limited spotted salamanders. Overall, our results indicate the effects of phenological variability on fitness-related traits can be modified or superseded by differences in density dependence. Identifying such context dependencies will lead to greater insight into when phenological variation will likely alter species interactions.

The influence of breeding phenology on the genetic structure of four pond-breeding salamanders.

Understanding metapopulation dynamics requires knowledge about local population dynamics and movement in both space and time. Most genetic metapopulation studies use one or two study species across the same landscape to infer population dynamics; however, using multiple co-occurring species allows for testing of hypotheses related to different life history strategies. We used genetic data to study dispersal, as measured by gene flow, in three ambystomatid salamanders (Ambystoma annulatum, A. maculatum, and A. opacum) and the Central Newt (Notophthalmus viridescens louisianensis) on the same landscape in Missouri, USA. While all four salamander species are forest dependent organisms that require fishless ponds to reproduce, they differ in breeding phenology and spatial distribution on the landscape. We use these differences in life history and distribution to address the following questions: (1) Are there species-level differences in the observed patterns of genetic diversity and genetic structure? and (2) Is dispersal influenced by landscape resistance? We detected two genetic clusters in A. annulatum and A. opacum on our landscape; both species breed in the fall and larvae overwinter in ponds. In contrast, no structure was evident in A. maculatum and N. v. louisianensis, species that breed during the spring. Tests for isolation by distance were significant for the three ambystomatids but not for N. v. louisianensis. Landscape resistance also contributed to genetic differentiation for all four species. Our results suggest species-level differences in dispersal ability and breeding phenology are driving observed patterns of genetic differentiation. From an evolutionary standpoint, the observed differences in dispersal distances and genetic structure between fall breeding and spring breeding species may be a result of the trade-off between larval period length and size at metamorphosis which in turn may influence the long-term viability of the metapopulation. Thus, it is important to consider life history differences among closely related and ecologically similar species when making management decisions.

Joint effects of resources and amphibians on pond ecosystems.

Primary production can be controlled through bottom-up (e.g., resources) or top-down (e.g., predators) constraints. Two key bottom-up resources in small aquatic systems are light and nutrients, and forest canopy cover heavily influences these factors, whereas amphibian and invertebrate colonizers exert top-down pressure as grazers and predators. We designed our experiment to specifically manipulate two different top-down and bottom-up factors. We manipulated resources by altering light (low/high) and nutrient (low/high) availability; omnivores with the presence/absence of southern leopard frog tadpoles (Lithobates sphenocephalus); and predators with the presence/absence of spotted salamander larvae (Ambystoma maculatum) in a full-factorial experiment conducted over 14 weeks. We observed that both bottom-up and top-down effects were important in predicting lower trophic level biomass. We found a significant top-down effect of salamanders on Daphnia, but tadpoles had the strongest overall effect on the food web, influencing phytoplankton (+), periphyton (-), and chironomids (-). None of our models were good predictors of phytoplankton biomass, but both shading and nutrient availability relatively equally boosted periphyton biomass. We also found large temporal differences in food-web dynamics. Our results underscore the need for more information into how ecosystem functioning could be altered by land use, amphibian extirpation, and climate change.