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USGS2018

Occupancy modeling species–environment relationships with non‐ignorable survey designs

Statistical models supporting inferences about species occurrence patterns in relation to environmental gradients are fundamental to ecology and conservation biology. A common implicit assumption is that the sampling design is ignorable and does not need to be formally accounted for in analyses. The analyst assumes data are representative of the desired population and statistical modeling proceeds. However, if data sets from probability and non‐probability surveys are combined or unequal selection probabilities are used, the design may be non‐ignorable. We outline the use of pseudo‐maximum likelihood estimation for site‐occupancy models to account for such non‐ignorable survey designs. This estimation method accounts for the survey design by properly weighting the pseudo‐likelihood equation. In our empirical example, legacy and newer randomly selected locations were surveyed for bats to bridge a historic statewide effort with an ongoing nationwide program. We provide a worked example using bat acoustic detection/non‐detection data and show how analysts can diagnose whether their design is ignorable. Using simulations we assessed whether our approach is viable for modeling data sets composed of sites contributed outside of a probability design. Pseudo‐maximum likelihood estimates differed from the usual maximum likelihood occupancy estimates for some bat species. Using simulations we show the maximum likelihood estimator of species–environment relationships with non‐ignorable sampling designs was biased, whereas the pseudo‐likelihood estimator was design unbiased. However, in our simulation study the designs composed of a large proportion of legacy or non‐probability sites resulted in estimation issues for standard errors. These issues were likely a result of highly variable weights confounded by small sample sizes (5% or 10% sampling intensity and four revisits). Aggregating data sets from multiple sources logically supports larger sample sizes and potentially increases spatial extents for statistical inferences. Our results suggest that ignoring the mechanism for how locations were selected for data collection (e.g., the sampling design) could result in erroneous model‐based conclusions. Therefore, in order to ensure robust and defensible recommendations for evidence‐based conservation decision‐making, the survey design information in addition to the data themselves must be available for analysts. Details for constructing the weights used in estimation and code for implementation are provided.

Ecological Applications↗

USGS2005

Assessment of shallow ground-water quality in recently urbanized areas of Sacramento, California, 1998

Evidence for anthropogenic impact on shallow ground-water quality beneath recently developed urban areas of Sacramento, California, has been observed in the sampling results from 19 monitoring wells in 1998. Eight volatile organic compounds (VOCs), four pesticides, and one pesticide transformation product were detected in low concentrations, and nitrate, as nitrogen, was detected in elevated concentrations; all of these concentrations were below National and State primary and secondary maximum contaminant levels. VOC results from this study are more consistent with the results from urban areas nationwide than from agricultural areas in the Central Valley, indicating that shallow ground-water quality has been impacted by urbanization. VOCs detected may be attributed to either the chlorination of drinking water, such as trichloromethane (chloroform) detected in 16 samples, or to the use of gasoline additives, such as methyl tert-butyl ether (MTBE), detected in 2 samples. Pesticides detected may be attributed to use on household lawns and gardens and rights-of-way, such as atrazine detected in three samples, or to past agricultural practices, and potentially to ground-water/surface-water interactions, such as bentazon detected in one sample from a well adjacent to the Sacramento River and downstream from where bentazon historically was used on rice. Concentrations of nitrate may be attributed to natural sources, animal waste, old septic tanks, and fertilizers used on lawns and gardens or previously used on agricultural crops. Seven sample concentrations of nitrate, as nitrogen, exceeded 3.0 milligrams per liter, a level that may indicate impact from human activities. Ground-water recharge from rainfall or surface-water runoff also may contribute to the concentrations of VOCs and pesticides observed in ground water. Most VOCs and pesticides detected in ground-water samples also were detected in air and surface-water samples collected at sites within or adjacent to the recently developed urban areas. Five arsenic sample concentrations exceeded the U.S. Environmental Protection Agency (USEPA) primary maximum contaminant level (MCL) of 10 milligrams per liter adopted in 2001. Measurements that exceeded USEPA or California Department of Health Services recommended secondary maximum contaminant levels include manganese, iron, chloride, total dissolved solids, and specific conductance. These exceedances are probably a result of natural processes. Variations in stable isotope ratios of hydrogen (2H/1H) and oxygen (18O/16O) may indicate different sources or a mixing of recharge waters to the urban ground water. These variations also may indicate recharge directly from surface water in one well adjacent to the Sacramento River. Tritium concentrations indicate that most shallow ground water has been recharged since the mid-1950s, and tritium/helium-3 age dates suggest that recharge has occurred in the last 2 to 30 years in some areas. In areas where water table depths exceed 20 meters and wells are deeper, ground-water recharge may have occurred prior to 1950, but low concentrations of pesticides and VOCs detected in these deeper wells indicate a mixing of younger and older waters. Overall, the recently urbanized areas can be divided into two groups. One group contains wells where few VOCs and pesticides were detected, nitrate mostly was not detected, and National and State maximum contaminant levels, including the USEPA MCL for arsenic, were exceeded; these wells are adjacent to rivers and generally are characterized by younger water, shallow (1 to 4 meters) water table, chemically reducing conditions, finer grained sediments, and higher organics in the soils. In contrast, the other group contains wells where more VOCs, pesticides, and elevated nitrate concentrations were detected; these wells are farther from rivers and are generally characterized by a mixture of young and old waters, intermediate to deep (7 to 35 meters) wate

Scientific Investigations Report↗

USGS1990

A proposal to conserve black-footed ferrets and the prairie dog ecosystem

Prairie dogs ( Cynomys spp.) have been poisoned throughout this century because of grazing competition with livestock. Recent evidence showed these early claims were exaggerated, but animal control was already entrenched in government policy. As a result, ongoing government subsidized poisoning has reduced prairie dogs to about 2% of their former distribution. The reduction of prairie dogs diminished species diversity in the arid grasslands of North America, including the potential extinction of the black-footed ferret ( Mustela nigripes ). Cost-benefit analysis revealed that poisoning costs more than any grazing benefits accrued. This analysis did not consider the long-term costs of reversing ecosystem degradation, the intangible value of biological diversity as a public benefit, or the depletion of biotic resources as a loss of actual or potential wealth. The government presently finances the poisoning policy and the preservation of endangered species like the black-footed ferret, two apparently conflicting programs. We, therefore, propose an integrated management plan that considers both interests. We propose that federal monies allocated to the poisoning program be converted into a rebate for ranchers who manage livestock while preserving the prairie dog community. This would redirect funds and personnel already allocated to prairie dog eradication to an incentive for ranchers who manage for livestock and wildlife. Livestock interests and grassland biotic diversity would both benefit.

Environmental Management↗

USGS2016

Evidence of estrogenic endocrine disruption in smallmouth and largemouth bass inhabiting Northeast U.S. National Wildlife Refuge waters: A reconnaissance study

Intersex as the manifestation of testicular oocytes (TO) in male gonochoristic fishes has been used as an indicator of estrogenic exposure. Here we evaluated largemouth bass ( Micropterus salmoides ) or smallmouth bass ( Micropterus dolomieu ) form 19 National Wildlife Refuges (NWRs) in the Northeast U.S. inhabiting waters on or near NWR lands for evidence of estrogenic endocrine disruption. Waterbodies sampled included rivers, lakes, impoundments, ponds, and reservoirs. Here we focus on evidence of endocrine disruption in male bass evidenced by gonad histopathology including intersex or abnormal plasma vitellogenin (Vtg) concentrations. During the fall seasons of 2008–2010, we collected male smallmouth bass ( n =118) from 12 sites and largemouth bass ( n =173) from 27 sites. Intersex in male smallmouth bass was observed at all sites and ranged from 60% to 100%; in male largemouth bass the range was 0–100%. Estrogenicity, as measured using a bioluminescent yeast reporter, was detected above the probable no effects concentration (0.73 ng/L) in ambient water samples from 79% of the NWR sites. Additionally, the presence of androgen receptor and glucocorticoid receptor ligands were noted as measured via novel nuclear receptor translocation assays. Mean plasma Vtg was elevated (>0.2 mg/ml) in male smallmouth bass at four sites and in male largemouth bass at one site. This is the first reconnaissance survey of this scope conducted on US National Wildlife Refuges. The baseline data collected here provide a necessary benchmark for future monitoring and justify more comprehensive NWR-specific studies.

Maine, Maryland, Massachusetts, New Hampshire, New↗

USGS2005

Retrospective ecotoxicological data and current information needs for terrestrial vertebrates residing in coastal habitat of the United States

The Contaminant Exposure and Effects—Terrestrial Vertebrates (CEE-TV) database was developed to conduct simple searches for ecotoxicological information, examine exposure trends, and identify significant data gaps. The CEE-TV database contains 16,696 data records on free-ranging amphibians, reptiles, birds, and mammals residing in estuarine and coastal habitats of the Atlantic, Gulf, and Pacific coasts, Alaska, Hawaii, and the Great Lakes. Information in the database was derived from over 1800 source documents, representing 483 unique species (about 252,000 individuals), with sample collection dates spanning from 1884 to 2003. The majority of the records contain exposure data (generally contaminant concentrations) on a limited number ( n = 209) of chlorinated and brominated compounds, cholinesterase-inhibiting pesticides, economic poisons, metals, and petroleum hydrocarbons, whereas only 9.3% of the records contain biomarker or bioindicator effects data. Temporal examination of exposure data provides evidence of declining concentrations of certain organochlorine pesticides in some avian species ( e.g. , ospreys, Pandion haliaetus ), and an apparent increase in the detection and possibly the incidence of avian die-offs related to cholinesterase-inhibiting pesticides. To identify spatial data gaps, 11,360 database records with specific sampling locations were combined with the boundaries of coastal watersheds, and National Wildlife Refuge and National Park units. Terrestrial vertebrate ecotoxicological data were lacking in 41.9% of 464 coastal watersheds in the continental United States. Recent (1990–2003) terrestrial vertebrate contaminant exposure or effects data were available for only about half of the National Wildlife Refuge and National Park units in the geographic area encompassed by the database. When these data gaps were overlaid on watersheds exhibiting serious water quality problems and/or high vulnerability to pollution, 72 coastal watersheds, and 76 National Wildlife Refuge and 59 National Park units in the continental United States were found to lack recent terrestrial vertebrate ecotoxicology data. Delineation of data gaps in watersheds of concern can help prioritize monitoring in areas with impaired water quality and emphasize the need for comprehensive monitoring to gain a more complete understanding of coastal ecosystem health.

Archives of Environmental Contamination and Toxico↗

USGS2011

Acute toxicity, histopathology, and coagulopathy in American kestrels (Falco sparverius) following administration of the rodenticie diphacinone

The acute oral toxicity of the anticoagulant rodenticide diphacinone was found to be over 20 times greater in American kestrels (Falco sparverius; median lethal dose 96.8 mg/kg body weight) compared with Northern bobwhite (Colinus virginianus) and mallards (Anas platyrhynchos). Modest evidence of internal bleeding was observed at necropsy, although histological examination of heart, liver, kidney, lung, intestine, and skeletal muscle revealed hemorrhage over a wide range of doses (35.1-675 mg/kg). Residue analysis suggests that the half-life of diphacinone in the liver of kestrels that survived was relatively short, with the majority of the dose cleared within 7 d of exposure. Several precise and sensitive clotting assays (prothrombin time, Russell's viper venom time, thrombin clotting time) were adapted for use in this species, and oral administration of diphacinone at 50 mg/kg increased prothrombin time and Russell?s viper venom time at 48 and 96 h postdose compared with controls. Prolongation of in vitro clotting time reflects impaired coagulation complex activity, and generally corresponded with the onset of overt signs of toxicity and lethality. In view of the toxicity and risk evaluation data derived from American kestrels, the involvement of diphacinone in some raptor mortality events, and the paucity of threshold effects data following short-term dietary exposure for birds of prey, additional feeding trials with captive raptors are warranted to characterize more fully the risk of secondary poisoning.

Environmental Toxicology and Chemistry↗

USGS2023

Climate change and pulse migration: Intermittent Chugach Inuit occupation of glacial fiords on the Kenai Coast, Alaska

For millennia, Inuit peoples of the Arctic and Subarctic have been challenged by the impacts of climate change on the abundance of key subsistence species. Responses to climate-induced declines in animal populations included switching to alternative food sources and/or migrating to regions of greater availability. We examine these dynamics for the Chugach Inuit (Sugpiat) people of southern coastal Alaska by synthesizing a large body of evidence from archeological sites, including radiocarbon dates and archaeofaunal assemblages, and by applying contemporary knowledge of glaciomarine ecosystems, spatial patterns of resource richness, and ocean-climate induced regime shifts in the Gulf of Alaska. We hypothesize that Chugach groups migrated from Cook Inlet and Prince William Sound to the Kenai Peninsula during periods of low sea surface temperatures (SSTs) to harvest harbor seals, which were seasonally aggregated near tidewater glaciers during pupping season, as well as piscivorous seabirds, Pacific cod, and other species that thrive under cool ocean conditions. During warming phases, the Chugach returned to Cook Inlet and Prince William Sound to fish for salmon and other species that abound during higher SSTs. Drivers of this coupled human-natural system of repeated (pulse) migration include the Pacific Decadal Oscillation (PDO), the dominant pattern of sea surface temperatures in the North Pacific that has been shown to generate step-like regime shifts in the marine food web; and coastal glaciers that structure the functioning of fiord ecosystems and support high levels of biological productivity. The culturally-constructed Chugach niche in the glaciomarine habitat of the Gulf of Alaska was based on intergenerationally transmitted ecological knowledge that enabled a resilient, mobile response to climate and resource variation.

Alaska↗

USGS2026

Exploring management options for moose at their southern range limits considering growing disease risk

1. Populations of cold-adapted species are increasingly vulnerable along their low-latitude range limits due to shifting environmental conditions, biotic interactions, and anthropogenic pressures. Managing these populations is particularly challenging because of complex ecological dynamics, conflicting stakeholder interests, and decision-making under uncertainty. 2. We explored population growth (λ) of moose ( Alces alces ) under different hypothetical management scenarios, simulating combinations of five hypothetical harvest levels with three levels of disease impact. 3. Facing current disease, the population could support multiple levels of conservative harvest. Under elevated levels of disease-caused mortality, projections indicated declines for all harvest scenarios. We projected increases across all harvest scenarios when overlap with white-tailed deer ( Odocoileus virginianus ) was hypothetically reduced and disease mortality in moose minimized. We investigated whether uncertainty in moose demographic parameters altered population trajectory, and found changes in adult fecundity and calf survival could alter harvest decisions when λ<1. 4. Practical implication . While moose population trajectories may remain stable under current conditions, management of white-tailed deer that reduces moose exposure to lethal parasites may provide the greatest utility in sustaining moose in New York given the potential for increased disease. Continued monitoring of population size, growth, and disease prevalence would inform sustainable moose harvest levels that balance social and ecological management considerations.

New York↗

USGS2007

Differences in phosphorus and nitrogen delivery to the Gulf of Mexico from the Mississippi River Basin

Seasonal hypoxia in the northern Gulf of Mexico has been linked to increased nitrogen fluxes from the Mississippi and Atchafalaya River Basins, though recent evidence shows that phosphorus also influences productivity in the Gulf. We developed a spatially explicit and structurally detailed SPARROW water-quality model that reveals important differences in the sources and transport processes that control nitrogen (N) and phosphorus (P) delivery to the Gulf. Our model simulations indicate that agricultural sources in the watersheds contribute more than 70% of the delivered N and P. However, corn and soybean cultivation is the largest contributor of N (52%), followed by atmospheric deposition sources (16%); whereas P originates primarily from animal manure on pasture and rangelands (37%), followed by corn and soybeans (25%), other crops (18%), and urban sources (12%). The fraction of in-stream P and N load delivered to the Gulf increases with stream size, but reservoir trapping of P causes large local- and regional-scale differences in delivery. Our results indicate the diversity of management approaches required to achieve efficient control of nutrient loads to the Gulf. These include recognition of important differences in the agricultural sources of N and P, the role of atmospheric N, attention to P sources downstream from reservoirs, and better control of both N and P in close proximity to large rivers. ?? 2008 American Chemical Society.

Environmental Science & Technology↗

USGS2023

Bivalve effects on the food web supporting delta smelt—A spatially intensive study of bivalve recruitment, biomass, and grazing rate patterns with varying freshwater outflow in 2019

Phytoplankton are an important and limiting food source in the Sacramento-San Joaquin Delta and San Francisco Bay. The decline of phytoplankton biomass is one potential factor in the decline of the protected Hypomesus transpacificus (delta smelt) and other pelagic organisms. The bivalves Corbicula fluminea and Potamocorbula amurensis (hereafter C. fluminea and P. amurensis , respectively) have been shown to control phytoplankton biomass in several locations throughout the San Francisco Bay and the Sacramento-San Joaquin Delta; therefore, knowledge of their distribution and population dynamics are of great interest. Here, we describe the distribution and dynamics of bivalve biomass using samples collected by the California Department of Water Resources (DWR) as part of the benthic monitoring program in 2019. One element of DWR’s and the Bureau of Reclamation’s Environmental Monitoring Program—the Generalized Random Tessellation Stratified (GRTS) program—examines the spatial and temporal extent of C. fluminea and P. amurensis control on phytoplankton. Historically, the GRTS program sampled 175 benthic stations (50 stations that are monitored every year and 125 randomly selected new stations that are changed yearly) throughout the Sacramento-San Joaquin Delta and northern San Francisco Bay (San Pablo and Suisun Bays) during one week in May and October. In 2019, only the 50 annually replicated stations were sampled. Corbicula fluminea and P. amurensis biomass and grazing rates had similar trends; therefore, the conclusions regarding biomass are applied to grazing rate data as well. Corbicula fluminea biomass decreased from May to October, whereas P. amurensis average biomass (reported increased from May (1 g ash-free-dry-tissue mass/square meter (g AFDM/m 2 ) to October (2 g AFDM/m 2 ). Although C. fluminea ’s average biomass was lower in October (10 gAFDM/m 2 ) than in May (20 gAFDM/m 2 ), the highest single biomass value was also observed in October (300 gAFDM/m 2 ). In both May and October, most stations that recorded high C. fluminea biomass values were located in the deep water (≥3 m of depth between the surface of the water and the surface of the substrate on the bottom) and were sampled in either rivers or sloughs. A relation between depth and biomass was not observed for P. amurensis . Both C. fluminea and P. amurensis recruitment (recruits are considered animals ≤2.5mm in length in this study and recruitment is the process of recruits successfully settled to the bottom) increased from May to October. The total number of C. fluminea recruits more than doubled from May to October, whereas P. amurensis total recruitment increased by 8-fold during the same period. Most P. amurensis recruits in May can be attributed to one station, whereas the recruits in October were found at 14 stations. A relation between number of recruits and station depth was not evident for either C. fluminea or P. amurensis .

California↗

USGS2011

Compositional zonation and cumulus processes in the Mount Mazama magma chamber, Crater Lake, Oregon

The 6845 ± 50 BP climactic eruption of Mount Mazama discharged 47 ± 9 km 3 of vertically zoned calc-alkaline magma, affording a virtually complete section through the chamber. Evidence for two andesitic parents with different trace-element (particularly Sr) and water contents is preserved in the ejecta. Prior to eruption, a dominant volume of rhyodacite was underlain successively by high-Sr andesite, high-Sr crystal mushes, and low-Sr crystal mushes. Intergranular liquids in the high-Sr magmas were probably richer in water than those in the low-Sr magmas. Thermal continuity throughout the ejecta favours eruption from a single, zoned reservoir. Insight into chamber development is given by preclimactic rhyodacitic lavas and tephra erupted between about 30,000 BP and the climactic eruption. The oldest of these lavas, contaminated derivatives of low-Sr magma, contain crystal-poor magmatic inclusions of low-Sr andesite; the youngest has inclusions of high-Sr andesite and, like rhyodacitic pumice in the climactic ejecta, is hybrid magma containing an admixed high-Sr component. A model for steady-state growth of the chamber is inferred whereby repeated recharge, first by low-Sr then high-Sr andesite (± basalt), builds up a cumulate succession, while derivative liquid fractionates convectively, segregates, and mixes with an incrementally growing silicic volume. The magma chamber at Mount Mazama may provide insight into the evolution of some granitoid plutons.

Oregon↗

USGS2014

Does water chemistry affect the dietary uptake and toxicity of silver nanoparticles by the freshwater snail Lymnaea stagnalis ?

Silver nanoparticles (AgNPs) are widely used in many applications and likely released into the aquatic environment. There is increasing evidence that Ag is efficiently delivered to aquatic organisms from AgNPs after aqueous and dietary exposures. Accumulation of AgNPs through the diet can damage digestion and adversely affect growth. It is well recognized that aspects of water quality, such as hardness, affect the bioavailability and toxicity of waterborne Ag. However, the influence of water chemistry on the bioavailability and toxicity of dietborne AgNPs to aquatic invertebrates is largely unknown. Here we characterize for the first time the effects of water hardness and humic acids on the bioaccumulation and toxicity of AgNPs coated with polyvinyl pyrrolidone (PVP) to the freshwater snail Lymnaea stagnalis after dietary exposures. Our results indicate that bioaccumulation and toxicity of Ag from PVP-AgNPs ingested with food are not affected by water hardness and by humic acids, although both could affect interactions with the biological membrane and trigger nanoparticle transformations. Snails efficiently assimilated Ag from the PVP-AgNPs mixed with diatoms (Ag assimilation efficiencies ranged from 82 to 93%). Rate constants of Ag uptake from food were similar across the entire range of water hardness and humic acid concentrations. These results suggest that correcting regulations for water quality could be irrelevant and ineffective where dietary exposure is important.

Environmental Pollution↗

USGS2004

Are brook trout streams in Western Virginia and Shenandoah National Park recovering from acidification?

Streamwater composition data obtained through periodic sampling of streams that support brook trout ( Salvelinus fontinalis ) in the mountains of western Virginia were examined for evidence of recovery from acidification during the 1988−2001 period. Measurements of sulfate deposition in precipitation indicate that sulfate deposition in the region declined approximately 40% between 1985 and 2000. While no significant regional trends in acid−base constituents were observed for the set ( n = 65) of western Virginia study streams, significant regional trends were observed for a subset ( n = 14) of streams in Shenandoah National Park (SNP). For the subset of SNP streams, the median increase in acid-neutralizing capacity (ANC) was 0.168 μequiv L -1 year -1 and the median decrease in sulfate concentration was −0.229 μequiv L -1 year -1 . Although these trends are consistent with recovery from acidification, the degree of apparent recovery is small compared to estimates of historic acidification in SNP streams and much less than observed in other, more northern regions in the United States. Correlation between sulfate concentration trends and current sulfate concentrations in streamwater suggests that recovery from stream acidification in the western Virginia region is determined by sulfur retention processes in watershed soils. A transient increase in nitrate concentrations that occurred among some western Virginia streams following forest defoliation by the gypsy moth ( Lymantria dispar ) complicates interpretation of the observed patterns of change in acid−base status.

Virginia↗

USGS2020

Atlantic salmon (Salmo salar) exposed to different preparatory photoperiods during smoltification show varying responses in gill Na+/K+-ATPase, salinity-specific mRNA transcription and ionocyte differentiation

Control of the parr-smolt transformation (or smoltification) is crucial for the husbandry and successful seawater (SW) transfer of Atlantic salmon ( Salmo salar ) reared in freshwater (FW) hatcheries. Photoperiod is an important environmental signal that initiates the complex physiological, morphological and behavioural changes that coincide with marine migration. While the use of long-day photoperiods to initiate smoltification has been well studied, this study investigated how three preparatory photoperiods in FW (LD 08:16, LD 12:12, LD 16:08) preceding exposure to 24-h light (LD 24:0) may influence or enhance smolt performance and growth post-SW transfer. After the photoperiod treatment phase (8 weeks), all groups were exposed to LD 24:0 for 8 weeks (FW) and then transferred to SW for a further 8 weeks. Exposure to LD 16:08 induced rapid development of smolt-related characteristics such as increased gill NKA activity, gill NKAα1b mRNA, and plasma cortisol, and decreased gill NKAα1a mRNA levels and condition factor through the 8-week treatment phase. Subsequent exposure to a LD 24:0 photoperiod resulted in a partial reversal of several of these characteristics, suggesting these fish went through a partial desmoltification. Exposure to LD 12:12 for 8 weeks prior to LD 24:0 elicited an intermediary response in smoltification attributes compared to LD 16:08 and LD 08:16. The LD 12:12 group adapted to SW and showed no negative effects on growth or physiological responses after transfer to SW. Exposure to a shortened photoperiod (LD 08:16) did not elicit any smoltification-related changes prior to LD 24:0, however, exposure to LD 24:0 increased gill NKA activity, plasma cortisol, changes in NKAα1a and NKAα1b mRNA, and the ratio of NKAα1b: NKAα1a. These results were confirmed by the expected changes in NKAα1a and NKAα 1b-positive immuno-reactive gill ionocytes. In summary, after exposure to LD 24:0 fish in the LD 08:16 group showed similar levels of change to those of the LD 16:08 group during the initial FW phase (prior to exposure to LD 24:0). After SW transfer, all groups were able to upregulate SW-specific NKAα1b mRNA and acclimate to SW, even though no increase in cortisol was evident. By the end of the study, there was no difference in SW growth among the groups. Overall, our data indicate that LD 16:08 advanced hypoosmoregulatory characteristics prior to LD 24:0 exposure. In addition, the physiological and molecular indicators measured in this group suggest that fish could have been transferred to SW immediately after 8 weeks in LD 16:08, with no added benefit of successive exposure to LD 24:0, which is typically used by industry to induce smoltification.

Aquaculture↗

USGS2017

Population dynamics of brown trout (Salmo trutta) in Spruce Creek Pennsylvania: A quarter-century perspective

We examined the relationship between density-independent and density-dependent factors on the demography of a dense, relatively unexploited population of brown trout in Spruce Creek Pennsylvania between 1985 and 2011. Individual PCAs of flow and temperature data elucidated groups of years with multiple high flow versus multiple low flow characteristics and high versus low temperature years, although subtler patterns of variation also were observed. Density and biomass displayed similar temporal patterns, ranging from 710 to 1,803 trout/ha and 76–263 kg/ha. We detected a significantly negative linear stock-recruitment relationship ( R 2 = .39) and there was no evidence that flow or water temperature affected recruitment. Both annual survival and the per-capita rate of increase ( r ) for the population varied over the study, and density-dependent mechanisms possessed the greatest explanatory power for annual survival data. Temporal trends in population r suggested it displayed a bounded equilibrium with increases observed in 12 years and decreases detected in 13 years. Model selection analysis of per-capita rate of increase data for age 1, and adults ( N = eight interpretable models) indicated that both density-dependent (five of eight) and negative density-independent processes (five of eight, i.e. high flows or temperatures), affected r . Recruitment limitation also was identified in three of eight models. Variation in the per-capita rate of increase for the population was most strongly affected by positive density independence in the form of increasing spring–summer temperatures and recruitment limitation. Model selection analyses describing annual variation in both mean length and mass data yielded similar results, although maximum w i values were low ranging from 0.09 to 0.23 (length) and 0.13 to 0.22 (mass). Density-dependence was included in 15 of 15 interpretable models for length and all ten interpretable models for mass. Similarly, positive density-independent effects in the form of increasing autumn–winter flow were present in seven of 15 interpretable models for length and five of ten interpretable models for mass. Negative density independent effects also were observed in the form of high spring–summer flows or temperatures ( N = 4), or high autumn–winter temperatures ( N = 1). Our analyses of the factors affecting population regulation in an introduced population of brown trout demonstrate that density-dependent forces affected every important demographic characteristic (recruitment, survivorship, the rate of increase, and size) within this population. However, density-independent forces in the form of seasonal variations in flow and temperature also helped explain annual variation in the per-capita rate of increase, and mean length and mass data. Consequently, population regulation within this population is driven by a complex of biotic and environmental factors, although it seems clear that density-dependent factors play a dominant role.

Pennsylvania↗

USGS2012

Factors associated with sources, transport, and fate of chloroform and three other trihalomethanes in untreated groundwater used for drinking water

Multiple lines of evidence for indicating factors associated with the sources, transport, and fate of chloroform and three other trihalomethanes (THMs) in untreated groundwater were revealed by evaluating low-level analytical results and logistic regression results for THMs. Samples of untreated groundwater from wells used for drinking water were collected from 1996-2007 from 2492 wells across the United States and analyzed for chloroform, bromodichloromethane, dibromochloromethane, and bromoform by a low-level analytical method implemented in April 1996. Using an assessment level of 0.02 μg/L, chloroform was detected in 36.5% of public-well samples and 17.6% of domestic-well samples, with most concentrations less than 1 μg/L. Brominated THMs occurred less frequently than chloroform but more frequently in public-well samples than domestic-well samples. For both public and domestic wells, THMs occurred most frequently in urban areas. Logistic regression analyses showed that the occurrence of THMs was related to nonpoint sources such as urban land use and to point sources like septic systems. The frequent occurrence and concentration distribution pattern of THMs, as well as their frequent co-occurrence with other organic compounds and nitrate, all known to have anthropogenic sources, and the positive associations between THM occurrence and dissolved oxygen and recharge indicate the recycling of water that contains THMs and other anthropogenic contaminants.

Environmental Science & Technology↗

USGS2021

Genomic signatures of thermal adaptation are associated with clinal shifts of life history in a broadly distributed frog

Temperature is a critical driver of ectotherm life-history strategies, whereby a warmer environment is associated with increased growth, reduced longevity and accelerated senescence. Increasing evidence indicates that thermal adaptation may underlie such life-history shifts in wild populations. Single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) can help uncover the molecular mechanisms of temperature-driven variation in growth, longevity and senescence. However, our understanding of these mechanisms is still limited, which reduces our ability to predict the response of non-model ectotherms to global temperature change. In this study, we examined the potential role of thermal adaptation in clinal shifts of life-history traits (i.e. life span, senescence rate and recruitment) in the Columbia spotted frog Rana luteiventris along a broad temperature gradient in the western United States. We took advantage of extensive capture–recapture datasets of 20,033 marked individuals from eight populations surveyed annually for 14–18 years to examine how mean annual temperature and precipitation influenced demographic parameters (i.e. adult survival, life span, senescence rate, recruitment and population growth). After showing that temperature was the main climatic predictor influencing demography, we used RAD-seq data (50,829 SNPs and 6,599 putative CNVs) generated for 352 individuals from 31 breeding sites to identify the genomic signatures of thermal adaptation. Our results showed that temperature was negatively associated with annual adult survival and reproductive life span and positively associated with senescence rate. By contrast, recruitment increased with temperature, promoting the long-term viability of most populations. These temperature-dependent demographic changes were associated with strong genomic signatures of thermal adaptation. We identified 148 SNP candidates associated with temperature including three SNPs located within protein-coding genes regulating resistance to cold and hypoxia, immunity and reproduction in ranids. We also identified 39 CNV candidates (including within 38 transposable elements) for which normalized read depth was associated with temperature. Our study indicates that both SNPs and structural variants are associated with temperature and could eventually be found to play a functional role in clinal shifts in senescence rate and life-history strategies in R. luteiventris . These results highlight the potential role of different sources of molecular variation in the response of ectotherms to environmental temperature variation in the context of global warming.

Journal of Animal Ecology↗

USGS2015

Identification of groundwater nitrate contamination from explosives used in road construction: Isotopic, chemical, and hydrologic evidence

Explosives used in construction have been implicated as sources of NO 3 – contamination in groundwater, but direct forensic evidence is limited. Identification of blasting-related NO 3 – can be complicated by other NO 3 – sources, including agriculture and wastewater disposal, and by hydrogeologic factors affecting NO 3 – transport and stability. Here we describe a study that used hydrogeology, chemistry, stable isotopes, and mass balance calculations to evaluate groundwater NO 3 – sources and transport in areas surrounding a highway construction site with documented blasting in New Hampshire. Results indicate various groundwater responses to contamination: (1) rapid breakthrough and flushing of synthetic NO 3 – (low δ 15 N, high δ 18 O) from dissolution of unexploded NH 4 NO 3 blasting agents in oxic groundwater; (2) delayed and reduced breakthrough of synthetic NO 3 – subjected to partial denitrification (high δ 15 N, high δ 18 O); (3) relatively persistent concentrations of blasting-related biogenic NO 3 – derived from nitrification of NH 4 + (low δ 15 N, low δ 18 O); and (4) stable but spatially variable biogenic NO 3 – concentrations, consistent with recharge from septic systems (high δ 15 N, low δ 18 O), variably affected by denitrification. Source characteristics of denitrified samples were reconstructed from dissolved-gas data (Ar, N 2 ) and isotopic fractionation trends associated with denitrification (Δδ 15 N/Δδ 18 O ≈ 1.31). Methods and data from this study are expected to be applicable in studies of other aquifers affected by explosives used in construction.

Environmental Science & Technology↗