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Bayesian adaptive survey protocols for resource management

Transparency in resource management decisions requires a proper accounting of uncertainty at multiple stages of the decision‐making process. As information becomes available, periodic review and updating of resource management protocols reduces uncertainty and improves management decisions. One of the most basic steps to mitigating anthropogenic effects on populations is determining if a population of a species occurs in an area that will be affected by human activity. Species are rarely detected with certainty, however, and falsely declaring a species absent can cause improper conservation decisions or even extirpation of populations. We propose a method to design survey protocols for imperfectly detected species that accounts for multiple sources of uncertainty in the detection process, is capable of quantitatively incorporating expert opinion into the decision‐making process, allows periodic updates to the protocol, and permits resource managers to weigh the severity of consequences if the species is falsely declared absent. We developed our method using the giant gartersnake ( Thamnophis gigas ), a threatened species precinctive to the Central Valley of California, as a case study. Survey date was negatively related to the probability of detecting the giant gartersnake, and water temperature was positively related to the probability of detecting the giant gartersnake at a sampled location. Reporting sampling effort, timing and duration of surveys, and water temperatures would allow resource managers to evaluate the probability that the giant gartersnake occurs at sampled sites where it is not detected. This information would also allow periodic updates and quantitative evaluation of changes to the giant gartersnake survey protocol. Because it naturally allows multiple sources of information and is predicated upon the idea of updating information, Bayesian analysis is well‐suited to solving the problem of developing efficient sampling protocols for species of conservation concern.

California↗

Water and endangered fish in the Klamath River Basin: Do Upper Klamath Lake surface elevation and water quality affect adult Lost River and Shortnose Sucker survival?

In the western United States, water allocation decisions often incorporate the needs of endangered fish. In the Klamath River basin, an understanding of temporal variation in annual survival rates of Shortnose Suckers Chasmistes brevirostris and Lost River Suckers Deltistes luxatus and their relation to environmental drivers is critical to water management and sucker recovery. Extinction risk is high for these fish because most individuals in the populations are approaching their maximum life span and recruitment of new fish into the adult populations has never exceeded mortality losses in the past 22 years. We used a time series of mark–recapture data from the years 1999–2021 to analyze the relationship between lake level, water quality covariates, and survival of adult Shortnose Suckers and two spawning populations of Lost River Suckers in Upper Klamath Lake, Oregon. We compared competing model hypotheses in a maximum likelihood framework using Akaike's information criterion and then ran the top environmental covariates in a Bayesian framework to estimate how much of the variation in survival was explained by these covariates as compared to random variation. The complementary analyses found almost unequivocal support for our base model without environmental covariates. Estimated adult sucker survival was high across the time series and consistent with sucker life history (mean annual survival = 0.82–0.91). This suggests that adult suckers were generally robust to interannual variation in lake levels as well as consistently poor water quality within the years of our data set. Recovery time is limited, as a declining survival trend for adult suckers in recent years may be due to the onset of senescence. The successful recovery of suckers in Upper Klamath Lake may rely on shifting research from the causes of adult mortality and its relationship with lake surface elevation to the causes of poor recruitment into adult populations.

California, Oregon↗

Comparison of traditional and molecular analytical methods for detecting biological agents in raw and drinking water following ultrafiltration

Aims: To compare the performance of traditional methods to quantitative polymerase chain reaction (qPCR) for detecting five biological agents in large-volume drinking-water samples concentrated by ultrafiltration (UF). Methods and Results: Drinking-water samples (100 l) were seeded with Bacillus anthracis, Cryptospordium parvum, Francisella tularensis, Salmonella Typhi, and Vibrio cholerae and concentrated by UF. Recoveries by traditional methods were variable between samples and between some replicates; recoveries were not determined by qPCR. Francisella tularensis and V. cholerae were detected in all 14 samples after UF, B. anthracis was detected in 13, and C. parvum was detected in 9 out of 14 samples. Numbers found by qPCR after UF were significantly or nearly related to those found by traditional methods for all organisms except for C. parvum. A qPCR assay for S. Typhi was not available. Conclusions: qPCR can be used to rapidly detect biological agents after UF as well as traditional methods, but additional work is needed to improve qPCR assays for several biological agents, determine recoveries by qPCR, and expand the study to other areas. Significance and Impact of the Study: To our knowledge, this is the first study to compare the use of traditional and qPCR methods to detect biological agents in large-volume drinking-water samples. ?? 2009 The Society for Applied Microbiology.

Journal of Applied Microbiology↗

Problems and methods involved in relating land use to ground-water quality

Efforts to relate shallow ground-water quality to the land use near a well lead to several statistical difficulties. These include potential uncertainty in land-use categorical data due to misclassification, data closure, distributional skewing, and spatial autocorrelation. Methods of addressing these problems are, respectively, the establishment of limits on minimum buffer radius, the estimation of contrasts, rank-based tests of association, and sub-sampling to prevent buffer overlap. Relations between the presence of purgeable organic compounds in ground water and land use are used to illustrate these problems and methods.

Journal of the American Water Resources Associatio↗

Elemental signatures in otoliths of hatchery rainbow trout (Oncorhynchus mykiss): Distinctiveness and utility fo detecting origins and movement

Otolith chemistry in freshwater has considerable potential to reveal patterns of origin and movement, which would benefit traditional fisheries management and provide a valuable tool to curb the spread of invasive and illicitly stocked species. We evaluated the relationship between otolith and water chemistry for five markers (Ba/Ca, Mn/Ca, Sr/ Ca, Zn/Ca, and 87 Sr/ 86 Sr) in rainbow trout (Oncorhynchus mykiss) using the existing hatchery system in Colorado and Wyoming, USA, to provide controlled, seminatural conditions. Otolith Ba/Ca, Sr/Ca, and 87 Sr/ 86 Sr reflected ambient levels, whereas Mn/Ca and Zn/Ca did not. Using only the markers correlated with water chemistry, we classified fish to their hatchery of origin with up to 96% accuracy when element and isotope data were used together. Large changes in 87Sr/ Sr were evident in otolith transects, although subtler changes in Sr/Ca were also detectable. Our results suggest the relatively few otolith markers that reflect ambient chemistry can discriminate among locations and track movements well enough to provide valuable insight in a variety of applied contexts.

Canadian Journal of Fisheries and Aquatic Sciences↗

Fluxes of water and solute in a coastal wetland sediment. 2. Effect of macropores on solute exchange with surface water

Chloride was highly concentrated relative to seawater in matrix porewater but was comparatively dilute in macropores. Concentration differences in pore-size classes declined with depth until indistinguishable below 10 cm. The segregated chloride distribution can be explained if recharge to the sediment occurred by downward infiltration in macropores and discharge occurred by an upward flux in matrix pores to satisfy evapotranspiration. Without disturbance by the downward infiltration flux in macropores, upward advection of chloride in matrix pores and evapoconcentration increased chloride concentrations in matrix pores to a level well above the concentration in seawater. The resulting high concentrations of chloride in matrix pores induced a large diffusive efflux of chloride into surface water that was sufficient to balance new input of chloride by infiltration of seawater in macropores (0.085 mmol Cl cm -2 day-1). Transport models that were constrained by water balance measurements at the field site explained both the exponential form of the vertical distribution of chloride in matrix pores and the rate of change in storage of chloride in sediment porewater over a one month period.

Journal of Hydrology↗

A geochemical model of the Platanares geothermal system, Honduras

Results of exploration drilling combined with results of geologic, geophysical, and hydrogeochemical investigations have been used to construct a geochemical model of the Platanares geothermal system, Honduras. Three coreholes were drilled, two of which produced fluids from fractured Miocene andesite and altered Cretaceous to Eocene conglomerate at 450 to 680 m depth. Large volume artesian flows of 160-165??C, predominantly bicarbonate water are chemically similar to, but slightly less saline than widespread boiling hot-spring waters. The chemistry of the produced fluid is dominated by equilibrium reactions in sedimentary rocks at greater depths and higher temperatures than those measured in the wells. Chemical, isotope, and gas geothermometers indicate a deep fluid temperature of 200-245??C and reflect a relatively short residence time in the fractures feeding the wells. Chloride-enthalpy relations as well as isotopic and chemical compositions of well discharges, thermal springs, and local cold waters support a conceptual model of ascending high-temperature (minimum 225??C) parent fluid that has cooled conductively to form the 160-165??C shallow (to 680 m) fluid encountered by the wells. The hot-spring waters are formed by boiling and steam loss from more or less conductively cooled parent fluid. The more dilute boiling spring waters (Cl = ???32 mg/kg) have cooled from > 225??C to about 160??C by conduction and from 160??C to 98??C by boiling. The most concentrated boiling spring waters (Cl = 37 mg/kg) have cooled from > 225??C to about 200??C by conduction and from 200??C to 98??C by boiling. Intermediate concentrations reflect mixed cooling paths. ?? 1991.

Journal of Volcanology and Geothermal Research↗

Infection and mortality in captive wild-trapped canvasback ducks

Fungal, bacterial and malarial infections, as well as malnutrition caused heavy mortality in a group of wild-trapped canvasbacks ( Aythya valisineria ) held in 10 × 3 × 2 m open water pens. Deaths occurred between 21 and 158 days after confinement and were associated with infections of Aspergillus fumigatus , Escherichia coli , Staphylococcus sp., Streptococcus sp., Klebsiella sp., Enterobacter sp., and Plasmodium sp. Infection and mortality was believed to result from reduced resistance associated with confinement. Fourteen canvasbacks released onto large ponds survived throughout the period during which the penned birds died.

Maryland, Virginia↗

Sedimentary petrology of a declining reef ecosystem, Florida reef tract (U.S.A.)

Petrologic evaluation of biogenic sediments collected shelf-wide along the Florida reef tract in 1989 revealed three principal components: coral, the calcareous green alga Halimeda, and mollusc. The dominant grain was dependent in part upon local morphology that controlled composition and vitality of the biota. Either Halimeda or mollusc grains prevailed in sands off the upper Keys. In the middle and lower Keys, Halimeda grains prevailed nearshore and coral grains offshore. Comparison with similar analyses of samples collected in 1952 and 1963 indicates that, over 37 years, the relative abundance of molluscan grains more than doubled in the upper Keys and that of particulate coral tripled in the middle Keys. These changes can be interpreted in the context of physical and biological events that affected Florida Keys reefs over that period of time. In the 1970s, outbreaks of extremely cold water killed even representatives of the hardiest coral species. In the 1980s, black-band and white-band diseases decimated the major reef-building acroporid corals, and the pivotal herbivore, Diadema antillarum, disappeared. Although Diadema is a major coral bioeroder, the sea urchin is also essential to healthy reef growth. The increase in coral debris in the middle Keys may be related to Hurricane Donna in 1960, but it is also consistent with the prediction of accelerated bioerosion by boring organisms in response to increased plankton productivity. Plankton productivity is stimulated by nutrients from Florida Bay and by well-documented eutrophication of nearshore environments. In the upper Keys, where reefs are somewhat removed from bay and nearshore influence, a relative decrease in coral debris over the 37 years may reflect proliferation of algae and algae-grazing molluscs as well as suppressed rates of bioerosion in the absence of Diadema. Human activities have substantially increased the natural flux of fixed nitrogen to coastal systems worldwide. Waters in the Florida Keys are no exception. Spatial and temporal trends in sediment constituents are compared to a previously published model that predicts the response of benthic biota to changes in nutrient supply. As adapted to interpret changes observed in reef-tract sediments, the model provides insights into the natural nutrient gradient along the Florida reef tract.

Journal of Coastal Research↗

Interactions between ground water and surface water in the Suwannee River basin, Florida

Ground water and surface water constitute a single dynamic system in roost parts of the Suwannee River basin due to the presence of karat features that facilitate the interaction between the surface and subsurface. Low radon-222 concentrations (below background levels) and enriched amounts of oxygen-18 and deuterium in ground water indicate mixing with surface water in parts of the basin. Comparison of surface water and regional ground water flow patterns indicate that boundaries for ground water basins typically do not coincide with surface water drainage subbasins. There are several areas in the basin where ground water flow that originates outside of the Suwannee River basin crosses surface water basin boundaries during both low-flow and high-flow conditions. In a study area adjacent to the Suwannee River that consists predominantly of agricultural land use, 18 wells tapping the Upper Floridan aquifer and 7 springs were sampled three times during 1990 through 1994 for major dissolved inorganic constituents, trace elements, and nutrients. During a period of above normal rainfall that resulted in high river stage and high ground water levels in 1991, the combination of increased amounts of dissolved organic carbon and decreased levels of dissolved oxygen in ground water created conditions favorable for the natural reduction of nitrate by denitrification reactions in the aquifer. As a result, less nitrate was discharged by ground water to the Suwannee River.

Journal of the American Water Resources Associatio↗

Hydrochemical evidence for mixing of river water and groundwater during high-flow conditions, lower Suwannee River basin, Florida, USA

Karstic aquifers are highly susceptible to rapid infiltration of river water, particularly during periods of high flow. Following a period of sustained rainfall in the Suwannee River basin, Florida, USA, the stage of the Suwannee River rose from 3.0 to 5.88 m above mean sea level in April 1996 and discharge peaked at 360 m 3 /s. During these high-flow conditions, water from the Suwannee River migrated directly into the karstic Upper Floridan aquifer, the main source of water supply for the area. Changes in the chemical composition of groundwater were quantified using naturally occurring geochemical tracers and mass-balance modeling techniques. Mixing of river water with groundwater was indicated by a decrease in the concentrations of calcium, silica, and 222 Rn; and by an increase in dissolved organic carbon (DOC), tannic acid, and chloride, compared to low-flow conditions in water from a nearby monitoring well, Wingate Sink, and Little River Springs. The proportion (fraction) of river water in groundwater ranged from 0.13 to 0.65 at Wingate Sink and from 0.5 to 0.99 at well W-17258, based on binary mixing models using various tracers. The effectiveness of a natural tracer in quantifying mixing of river water and groundwater was related to differences in tracer concentration of the two end members and how conservatively the tracer reacted in the mixed water. Solutes with similar concentrations in the two end-member waters (Na, Mg, K, Cl, SO 4 , SiO 2 ) were not as effective tracers for quantifying mixing of river water and groundwater as those with larger differences in end-member concentrations (Ca, tannic acid, DOC, 222 Rn, HCO 3 ).

Hydrogeology Journal↗

The economic value of Trinity River water

The Trinity River, largest tributary of the Klamath River, has its head-waters in the Trinity Alps of north-central California. After the construction of Trinity Dam in 1963, 90% of the Trinity River flow at Lewiston was moved to the Sacramento River via the Clear Creek Tunnel, a manmade conduit. Hydropower is produced at four installations along the route of Trinity River water that is diverted to the Sacramento River, and power production at three of these installations would diminish if no Trinity River water were diverted to the Sacramento River. After Trinity River water reaches the Sacramento River, it flows toward the Sacramento-San Joaquin Delta and San Francisco Bay. Trinity River water is pumped via Bureau of Reclamation canals and pumps to the northern San Joaquin Valley, where it is used for irrigated agriculture. The social cost of putting more water down the Trinity River is the sum of the value of the foregone consumer surplus from hydropower production as well as the value of the foregone irrigation water. Sharply diminished instream flows have also severely affected the size and robustness of Trinity River salmon, steelhead, shad and sturgeon runs. Survey data were used to estimate the non-market benefits of augmenting Trinity River instream flows by letting more water flow down the Trinity and moving less water to the Sacramento River. Preservation benefits for Trinity River instream flows and fish runs are $803 million per annum for the scenario that returns the most water down the Trinity River, a value that greatly exceeds the social cost estimate.The Trinity River, largest tributary of the Klamath River, has its headwaters in the Trinity Alps of north-central California. After the construction of Trinity Dam in 1963, 90% of the Trinity River flow at Lewiston was moved to the Sacramento River via the Clear Creek Tunnel, a manmade conduit. Hydropower is produced at four installations along the route of Trinity River water that is diverted to the Sacramento River, and power production at three of these installations would diminish if no Trinity River water were diverted to the Sacramento River. After Trinity River water reaches the Sacramento River, it flows toward the Sacramento-San Joaquin Delta and San Francisco Bay. Trinity River water is pumped via Bureau of Reclamation canals and pumps to the northern San Joaquin Valley, where it is used for irrigated agriculture. The social cost of putting more water down the Trinity River is the sum of the value of the foregone consumer surplus from hydropower production as well as the value of the foregone irrigation water. Sharply diminished instream flows have also severely affected the size and robustness of Trinity River salmon, steelhead, shad and sturgeon runs. Survey data were used to estimate the non-market benefits of augmenting Trinity River instream flows by letting more water flow down the Trinity and moving less water to the Sacramento River. Preservation benefits for Trinity River instream flows and fish runs are $803 million per annum for the scenario that returns the most water down the Trinity River, a value that greatly exceeds the social cost estimate.

International Journal of Water Resources Developme↗

A new instrument for sampling flocculent material at the water/sediment interface

We have designed an instrument to collect fine-grained and flocculent material from the water/sediment interface for chemical and mineralogical analysis. The sampler can be used from a manned research submersible or by a diver in shallow water. In areas of active deposition, the material collected represents the most recently deposited sediment. This material is of interest for determining the concentration of anthropogenic contaminants at the sea floor and may be a much more sensitive indicator of early contamination than are bulk samples collected by means of conventional grab samplers or corers. The instrument also may be well suited for sampling freshly flocculated or precipitated material from the sea floor, for example in estuaries or around thermal vents on mid ocean ridges.

Journal of Sedimentary Research↗

Ecological distribution and crude density of breeding birds on prairie wetlands

Breeding populations of 28 species of wetland-dwelling birds other than waterfowl (Anatidae) were censused on 1,321 wetlands lying within the prairie pothole region of North Dakota. Ecological distribution and two crude measures of relative density were calculated for the 22 commonest species using eight wetland classes. Semipermanent wetlands supported nearly two-thirds of the population and were used by all 22 species, whereas seasonal wetlands contained about one-third of the population and were used by 20 species Semipermanent, fen, and temporary wetlands contained highest bird densities on the basis of wetland area; on the basis of wetland unit, densities were highest on semipermanent, permanent, alkali, and fen wetlands. The highest ranking of semipermanent wetlands by all three measures of use was probably because these wetlands, as well as being relatively numerous and large, were vegetatively diverse. The fairly large proportion of the bird population supported by seasonal wetlands was a result of wetland abundance and moderate vegetative diversity. Increased vegetative diversity results from the development of characteristic zones of hydrophytes at sites where water persists longer during the growing season. Frequent cultivation of prairie wetlands results in the replacement of tall, robust perennials by bare soil or stands of short, weak-stemmed annuals that likely are unattractive to nesting birds.

North Dakota↗

Anomalous spawning of smallmouth bass in Nebish Lake, Wisconsin: Implications for early spawning and over-winter survival

We observed that the smallmouth bass ( Micropterus dolomieu ) population in Nebish Lake, Wisconsin spawned twice-once during the traditional spring period and then again in summer, well beyond the typical spawning season for north-temperate lakes. We documented this anomalous spawning behavior and compared the characteristics of smallmouth bass nests built during the two distinct spawning seasons. Smallmouth bass built 463 nests (110.2 nests/km shoreline) as water temperature was rising toward 20°C. During the summer spawning period, 24 nests (5.7 nests/km shoreline) were constructed between 11 August and 29 August as water temperature was falling. Nests built in summer were significantly farther from shore, in deeper water, farther from cover, larger in diameter, and built by larger males than in the spring.

Wisconsin↗

Heterogeneous redox conditions, arsenic mobility, and groundwater flow in a fractured-rock aquifer near a waste repository site in New Hampshire, USA

Anthropogenic sources of carbon from landfill or waste leachate can promote reductive dissolution of in situ arsenic (As) and enhance the mobility of As in groundwater. Groundwater from residential-supply wells in a fractured crystalline-rock aquifer adjacent to a Superfund site in Raymond, New Hampshire, USA, showed evidence of locally enhanced As mobilization in relatively reducing (mixed oxic-anoxic to anoxic) conditions as determined by redox classification and other lines of evidence. Redox classification was determined from geochemical indicators based on threshold concentrations of dissolved oxygen (DO), nitrate (NO 3- ), iron (Fe 2+ ), manganese (Mn 2+ ), and sulfate (SO 4 2- ). Redox conditions were evaluated also based on methane (CH 4 ), excess nitrogen gas (N 2 ) from denitrification, the oxidation state of dissolved As speciation (As(III) and As(V)), and several stable isotope ratios. Samples from the residential-supply wells primarily exhibit mixed redox conditions, as most have long open boreholes (typically 50–100 m) that receive water from multiple discrete fractures with contrasting groundwater chemistry and redox conditions. The methods employed in this study can be used at other sites to gauge redox conditions and the potential for As mobilization in complex fractured crystalline-rock aquifers where multiple lines of evidence are likely needed to understand As occurrence, mobility, and transport.

New Hampshire↗

Linear model describing three components of flow in karst aquifers using 18O data

The stable isotope of oxygen, 18O, is used as a naturally occurring ground-water tracer. Time-series data for ??18O are analyzed to model the distinct responses and relative proportions of the conduit, intermediate, and diffuse flow components in karst aquifers. This analysis also describes mathematically the dynamics of the transient fluid interchange between conduits and diffusive networks. Conduit and intermediate flow are described by linear-systems methods, whereas diffuse flow is described by mass-balance methods. An automated optimization process estimates parameters of lognormal, Pearson type III, and gamma distributions, which are used as transfer functions in linear-systems analysis. Diffuse flow and mixing parameters also are estimated by these optimization methods. Results indicate the relative proximity of a well to a main conduit flowpath and can help to predict the movement and residence times of potential contaminants. The three-component linear model is applied to five wells, which respond to changes in the isotopic composition of point recharge water from a sinking stream in the Madison aquifer in the Black Hills of South Dakota. Flow velocities as much as 540 m/d and system memories of as much as 71 years are estimated by this method. Also, the mean, median, and standard deviation of traveltimes; time to peak response; and the relative fraction of flow for each of the three components are determined for these wells. This analysis infers that flow may branch apart and rejoin as a result of an anastomotic (or channeled) karst network.

Journal of Hydrology↗

Reexamining the Honolulu Volcanics: Hawai‘i's classic case of rejuvenation volcanism

Rejuvenated volcanism is a worldwide phenomenon occurring on many oceanic islands in all of the major ocean basins. This plume-related volcanism follows the main edifice-building stage after a hiatus of variable duration (e.g. 0.6–2 Myrs in Hawai'i). The Honolulu Volcanics (HV), the classic case of rejuvenated volcanism, involved monogenetic eruptions from at least 48 vent areas. Previous studies inferred these vents were aligned along 3 to 11 rifts oriented orthogonal to the propagation direction of the Hawaiian plume. HV basalts are known for having high MgO contents (greater than 10 wt %) and upper mantle xenoliths. Thus, HV magmas are assumed to be relatively primitive and to have ascended rapidly (less than 1 day) through the crust. However, new analyses of olivine cores in basalts from 24 HV vents are mostly too low in forsterite content (74–86 mol %) to be in equilibrium with mantle melts. Olivine and clinopyroxene in HV basalts commonly show reverse zoning indicating magma mixing prior to eruption. These results are inconsistent with the rapid ascent of HV magmas directly from their mantle source. Many of the HV magmas underwent storage (probably in the lower crust or uppermost mantle), crystal fractionation and magma mixing prior to eruption. New 40 Ar/ 39 Ar dates were determined for 11 HV lavas to evaluate their eruptive history. These ages, 80 to 685 ka, combined with our previous and other 40 Ar/ 39 Ar ages for HV lavas reveal long gaps (greater than 50 kyr) between some eruptions. Our comprehensive, whole-rock major and trace element database (63 XRF analyses, 57 ICPMS analyses) of basalts from 37 vents show remarkable compositional diversity with no obvious spatial pattern or temporal trends. The two most recent eruptive sequences have the greatest diversity (basanite and melilitite compositions). HV basanites show systematic trace element trends that may reflect mixing of multiple source components. The nephelinites and melilitites require a complex source history that may have involved residual accessory minerals during mantle melting and a metasomatic component that was not carbonatitic. The new ages and geochemical data show eruptions along most of the previously proposed rift systems were unrelated (except for the Koko Rift). Therefore, geodynamic models that relate HV volcanism to these rift systems are invalid. Lava volumes for two HV eruptions were estimated at 0.11 and 0.23 km 3 using surface mapping and water well data. Similar size, recent monogenetic eruptions in Auckland, New Zealand, were inferred to have lasted several months. Thus, if another HV eruption were to occur, which is possible given the long hiatus between eruptions, it would be extremely disruptive for the nearly 1 million residents of Honolulu. None of the existing geodynamic models fully explain the age duration, volumes and the locations of Hawai'i's rejuvenated volcanism. Thus, the cause of this secondary volcanism remains enigmatic.

Hawaii↗