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Common loons (Gavia immer) are at risk of elevated dietary mercury (Hg) exposure in portions of their breeding range. To assess the level of risk among loons in Minnesota (USA), we investigated loon blood Hg concentrations in breeding lakes across Minnesota. Loon blood Hg concentrations were regressed on predicted Hg concentrations in standardized 12-cm whole-organism yellow perch (Perca flavescens), based on fish Hg records from Minnesota lakes, using the US Geological Survey National Descriptive Model for Mercury in Fish. A linear model, incorporating common loon sex, age, body mass, and log-transformed standardized perch Hg concentration representative of each study lake, was associated with 83% of the variability in observed common loon blood Hg concentrations. Loon blood Hg concentration was positively related to standardized perch Hg concentrations; juvenile loons had lower blood Hg concentrations than adult females, and blood Hg concentrations of juveniles increased with body mass. Blood Hg concentrations of all adult common loons and associated standardized prey Hg for all loon capture lakes included in the study were well below proposed thresholds for adverse effects on loon behavior, physiology, survival, and reproductive success. The fish Hg modeling approach provided insights into spatial patterns of dietary Hg exposure risk to common loons across Minnesota. We also determined that loon blood selenium (Se) concentrations were positively correlated with Hg concentration. Average common loon blood Se concentrations exceeded the published provisional threshold. Environ Toxicol Chem 2019;38:524-532. Published 2018 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.

Floodplain forests of large rivers in the midwestern United States are naturally fragmented by sloughs, backwaters, wetlands, and shrub carr. On the highly altered Upper Mississippi River (UMR), resource managers want to protect and manage floodplain forests to benefit forest “interior” bird species. To discover bird relations with interior and edge floodplain forest, we characterized bird assemblages during spring migration and breeding season in 3 forest types: habitat in the interior of forest areas > 100 m from an edge, edges associated with interior areas, and other areas of forest not associated with an interior area (random sites) on the UMR between Hastings and Red Wing, Minnesota. The random sites represent the majority of UMR floodplain forest area because only a small percentage of forest occurs >100 m from edge. Estimated habitat characteristics did not differ among interior, edge, and random sites. Bird relative abundance, species richness, diversity, assemblage composition, and detections of all but one species (in spring) did not differ among interior, edge, and random sites during both seasons. Our results suggest a homogeneous bird assemblage across UMR floodplain forest in the study area during spring migration and the breeding season, and that individual forest bird species do not seem to be more abundant in interior or edge areas as we defined them.

Pool‐scale growing‐season water‐level reductions (drawdowns) have been implemented on the Upper Mississippi River in an effort to improve fish and wildlife habitat. Aquatic vegetation is a key habitat component, with perennial emergent species, such as Sagittaria latifolia and Sagittaria rigida, especially important. River managers have assumed the need for continuous drawdown during the growing season with limited reflooding and used this guidance in assessing the potential for an ecologically successful drawdown. However, information on the effects of growing‐season flooding episodes on survival and growth of Sagittaria is limited. To assess the flooding tolerance of S. latifolia and S. rigida, we evaluated multiple levels of timing, duration, and depth on survival and productivity of plants. Plants were produced from S. latifolia and S. rigida seeds and S. latifolia tubers; all were reared under moist‐soil or shallow‐flooded rearing conditions. Mortality of plants was low (2%) among plants from large tubers, low (7%) among seedlings (and largely associated with early flooding treatments), and modest (11%) among plants from small tubers (with no clear effects of inundation). Flooding treatments generally had a positive effect on biomass production from seedlings, particularly when treatments occurred early, were relatively shallow, and were short in duration. There were no clear effects of depth, duration, or timing components of flooding treatments on plant biomass arising from tubers. This experiment indicates that S. latifolia and S. rigida are relatively tolerant of flooding events during the growing season and may actually benefit from some level of inundation.

Common loons (Gavia immer) staging on the Great Lakes during fall migration are at risk to episodic outbreaks of type E botulism. Information on distribution, foraging patterns, and exposure routes of loons are needed for understanding the physical and ecological factors that contribute to avian botulism outbreaks. Aerial surveys were conducted to document the spatiotemporal distribution of common loons on Lake Michigan during falls 2011–2013. In addition, satellite telemetry and archival geolocator tags were used to determine the distribution and foraging patterns of individual common loons while using Lake Michigan during fall migration. Common loon distribution observed during aerial surveys and movements of individual radiomarked and/or geotagged loons suggest a seasonal pattern of use, with early fall use of Green Bay and northern Lake Michigan followed by a shift in distribution to southern Lake Michigan before moving on to wintering areas. Common loons tended to occupy offshore areas of Lake Michigan and, on average, spent the majority of daylight hours foraging. Dive depths were as deep as 60 m and dive characteristics suggested that loons were primarily foraging on benthic prey. A recent study concluded that round gobies (Neogobius melanostomus) are an important prey item of common loons and may be involved in transmission of botulinum neurotoxin type E. Loon distribution coincides with the distribution of dreissenid mussel biomass, an important food resource for round gobies. Our observations support speculation that energy transfer to higher trophic levels via gobies may occur in deep-water habitats, along with transfer of botulinum neurotoxin.

The invasive sea lamprey ( Petromyzon marinus ) poses a substantial threat to fish communities in the Great Lakes. Efforts to control sea lamprey populations typically involve treating tributary streams with lampricides on a recurring cycle. The presence of a substantial population of larval sea lampreys in the aquatic corridor between Lakes Huron and Erie prompted managers to propose a treatment using the granular formulation of Bayluscide® that targets larval sea lampreys that reside in sediments. However, these treatments could cause adverse effects on native freshwater mussels—imperiled animals that also reside in sediments. We estimated the risk of mortality and sub-lethal effects among eight species of adult and sub-adult mussels exposed to Bayluscide® for durations up to 8 h to mimic field applications. Mortality was appreciable in some species, especially in sub-adults (range, 23–51%). The lethal and sub-lethal effects were positively associated with the duration of exposure in most species and life stage combinations. Estimates of the median time of exposure that resulted in lethal and sub-lethal effects suggest that sub-adults were often affected by Bayluscide® earlier than adults. Siphoning activity and burrowing position of mussels during exposure may have moderated the uptake of Bayluscide® and may have influenced lethal and sub-lethal responses. Given that the various species and life stages were differentially affected, it will be difficult to predict the effects of Bayluscide® treatments on mussels.

Floodplain forest of the Upper Mississippi River provides habitat for an abundant and diverse breeding bird community. However, reed canary grass Phalaris arundinacea invasion is a serious threat to the future condition of this forest. Reed canary grass is a well-known aggressive invader of wetland systems in the northern tier states of the conterminous United States. Aided by altered flow regimes and nutrient inputs from agriculture, reed canary grass has formed dense stands in canopy gaps and forest edges, retarding tree regeneration. We sampled vegetation and breeding birds in Upper Mississippi River floodplain forest edge and interior areas to 1) measure reed canary grass cover and 2) evaluate whether the breeding bird assemblage responded to differences in reed canary grass cover. Reed canary grass was found far into forest interiors, and its cover was similar between interior and edge sites. Bird assemblages differed between areas with more or less reed canary grass cover (>53% cover breakpoint). Common yellowthroat Geothlypis trichas, black-capped chickadee Parus atricapillus, and rose-breasted grosbeak Pheucticus ludovicianus were more common and American redstart Setophaga ruticilla, great crested flycatcher Myiarchus crinitus, and Baltimore oriole Icterus galbula were less common in sites with more reed canary grass cover. Bird diversity and abundance were similar between sites with different reed canary grass cover. A stronger divergence in bird assemblages was associated with ground cover

Trend estimates are often used as part of environmental monitoring programs. These trends inform managers (e.g., are desired species increasing or undesired species decreasing?). Data collected from environmental monitoring programs is often aggregated (i.e., averaged), which confounds sampling and process variation. State-space models allow sampling variation and process variations to be separated. We used simulated time-series to compare linear trend estimations from three state-space models, a simple linear regression model, and an auto-regressive model. We also compared the performance of these five models to estimate trends from a long term monitoring program. We specifically estimated trends for two species of fish and four species of aquatic vegetation from the Upper Mississippi River system. We found that the simple linear regression had the best performance of all the given models because it was best able to recover parameters and had consistent numerical convergence. Conversely, the simple linear regression did the worst job estimating populations in a given year. The state-space models did not estimate trends well, but estimated population sizes best when the models converged. We found that a simple linear regression performed better than more complex autoregression and state-space models when used to analyze aggregated environmental monitoring data.

Levels of submersed aquatic vegetation (SAV) are commonly assessed using a modified garden rake. However, the utility of the rake sampling method relative to methods that are typically viewed as more definitive (and expensive) such as snorkeling and coring remains a matter of debate. This study explores whether probabilities of species detections for four SAV species varied among sampling units in a rake-biomass study and, if so, whether such variation reflected variation in species abundance. Variation in detection probabilities, when unaddressed, may yield biased estimators of percent frequency of occurrence (“occupancy”) and of occurrence-habitat associations. Biomass-driven variation in detection probabilities is important because such variation may not be explainable using covariates typically measured when sampling using the rake method. This study found substantial among-unit variation in detection probabilities, with majorities of that variation on the logit or modeling scale being associated with biomass but not with the non-biomass covariates substrate type, water depth and day of study. The study closes by exploring sampling protocols and modeling methods that may yield improved SAV occupancy estimates.

Long-term temporal trends in water temperature in rivers and streams are typically estimated under the assumption of evenly-spaced space-time measurements. However, sampling times and dates associated with historical water temperature datasets and some sampling designs may be haphazard. As a result, trends in temperature may be confounded with trends in time or space of sampling which, in turn, may yield biased trend estimators and thus unreliable conclusions. We address this concern using multilevel (hierarchical) linear models, where time effects are allowed to vary randomly by day and date effects by year. We evaluate the proposed approach by Monte Carlo simulations with imbalance, sparse data and confounding by trend in time and date of sampling. Simulation results indicate unbiased trend estimators while results from a case study of temperature data from the Illinois River, USA conform to river thermal assumptions. We also propose a new nonparametric bootstrap inference on multilevel models that allows for a relatively flexible and distribution-free quantification of uncertainties. The proposed multilevel modeling approach may be elaborated to accommodate nonlinearities within days and years when sampling times or dates typically span temperature extremes.

A field study was conducted in Wisconsin (USA) to characterize in ovo mercury (Hg) exposure in common loons (Gavia immer). Total Hg mass fractions ranged from 0.17 µg/g to 1.23 µg/g wet weight in eggs collected from nests on lakes representing a wide range of pH (5.0–8.1) and were modeled as a function of maternal loon Hg exposure and egg laying order. Blood total Hg mass fractions in a sample of loon chicks ranged from 0.84 µg/g to 3.86 µg/g wet weight at hatch. Factors other than mercury exposure that may have persistent consequences on development of chicks from eggs collected on low-pH lakes (i.e., egg selenium, calcium, and fatty acid mass fractions) do not seem to be contributing to reported differences in loon chick quality as a function of lake pH. However, it was observed that adult male loons holding territories on neutral-pH lakes were larger on average than those occupying territories on low-pH lakes. Differences in adult body size of common loons holding territories on neutral-versus low-pH lakes may have genetic implications for differences in lake-source-related quality (i.e., size) in chicks. The tendency for high in ovo Hg exposure and smaller adult male size to co-occur in low-pH lakes complicates the interpretation of the relative contributions of each to resulting chick quality. Environ Toxicol Chem 2015;34:1870–1880. © 2015 SETAC

The whooping crane Grus americana has a long conservation history, but despite multiple attempts across North America, introduction success is lacking. Recently introduced, captively reared whooping cranes have had periods of poor reproductive performance in central Wisconsin that sometimes coincided with black fly (Diptera: Simuliidae) emergences. Sandhill crane Grus canadensis reproductive performance in central Wisconsin is approximately double that of whooping cranes. We used comfort behaviors as a measure of black fly harassment to infer whether behavioral differences existed between nesting sandhill cranes and nesting whooping cranes and between successful and unsuccessful whooping crane pairs. To further explore the interaction between black flies and incubating whooping cranes, we examined differences in behaviors between incubating birds and their off-nest mates. Compared to their off-nest mates, incubating whooping cranes exhibited elevated comfort behaviors, suggesting a bird at a nest may experience greater harassment from black flies. Sandhill cranes had elevated head-flicks over whooping cranes. Whooping cranes exhibited more head-rubs than sandhill cranes, and successful whooping crane pairs had elevated head-rubs over pairs that deserted their nests. Behavioral differences between sandhill cranes and whooping cranes as well as differences in reproductive performance, could be explained by exposure to local breeding conditions. Whereas sandhill cranes have nested in the area for hundreds, if not thousands, of years, whooping cranes were only recently introduced to the area. Behavioral differences between the species as well as those between successful and unsuccessful whooping crane pairs could also be explained by the effect of captive exposure, which could affect all whooping crane introductions.

Summary Managers in the Upper Mississippi River (UMR) are using reductions in the River's water levels during summer to mimic historical water regimes and rehabilitate habitats for vegetation and other species. Concerns for the unintended effects of these actions on mussel populations threatened to halt these projects. Our objective was to characterise the survival and movement of two mussel species in the UMR associated with a water level drawdown. During 2009 (no drawdown) and 2010 (0.3 m summer drawdown), we glued passive integrated transponder tags to 10 Amblema plicata and 10 Lampsilis cardium at each of 11 sites. Five sites were in shallow areas expected to be minimally affected by the drawdown (reference sites), and six sites were in shallow areas expected to be directly affected by the drawdown (treatment sites). About equal numbers of sites within both the reference and treatment areas had low and high slopes. Tagged mussels were randomly allocated across sites (within years). Recovery of tagged mussels was >88% in 2009 and 2010. Mortality was similar and low (mean, c. 5% in both species) among reference sites but was variable and relatively high (means, c. 27% in L. cardium and c. 52% in A. plicata) among treatment sites; variation in mortality among treatment sites appeared related to slope. The study found evidence of drawdown associations with net horizontal movements in A. plicata but not L. cardium. Weekly horizontal movements in both species were significantly correlated with changes in water elevation. We observed significant slope associations related to the drawdown for mortality and net horizontal movement in A. plicata. There were strong species-specific differences in the effects of the drawdown on mortality, vertical movement and horizontal movement. These results suggest that A. plicata responded to the drawdown by vertical movement into the substratum, whereas L. cardium responded by horizontal movement to deeper water. No directionality of movement was observed in either species. Collectively, these data suggest that drawdowns can influence the mortality, movement and behaviour of mussels in the UMR. However, more information on spatial and temporal distributions of mussels is needed to better understand the magnitude of these effects. Results from this study are being used by resource managers to better evaluate the effects of this management tool on native mussel assemblages.

Mercury (Hg) contamination of fisheries is a major concern for resource managers of many temperate lakes. Anthropogenic Hg contamination is largely derived from atmospheric deposition within a lake's watershed, but its incorporation into the food web is facilitated by bacterial activity in sediments. Temporal variation in Hg content of fish (young-of-year yellow perch) in the regulated lakes of the Rainy-Namakan complex (on the border of the United States and Canada) has been linked to water level (WL) fluctuations, presumably through variation in sediment inundation. As a result, Hg contamination of fish has been linked to international regulations of WL fluctuation. Here we assess the relationship between WL fluctuations and fish Hg content using a 10-year dataset covering six lakes. Within-year WL rise did not appear in strongly supported models of fish Hg, but year-to-year variation in maximum water levels (∆maxWL) was positively associated with fish Hg content. This WL effect varied in magnitude among lakes: In Crane Lake, a 1 m increase in ∆maxWL from the previous year was associated with a 108 ng increase in fish Hg content (per gram wet weight), while the same WL change in Kabetogama was associated with only a 5 ng increase in fish Hg content. In half the lakes sampled here, effect sizes could not be distinguished from zero. Given the persistent and wide-ranging extent of Hg contamination and the large number of regulated waterways, future research is needed to identify the conditions in which WL fluctuations influence fish Hg content.

Site occupancy models are commonly used by ecologists to estimate the probabilities of species site occupancy and of species detection. This study addresses the influence on site occupancy and detection estimates of variation in species availability among surveys within sites. Such variation in availability may result from temporary emigration, nonavailability of the species for detection, and sampling sites spatially when species presence is not uniform within sites. We demonstrate, using Monte Carlo simulations and aquatic vegetation data, that variation in availability and heterogeneity in the probability of availability may yield biases in the expected values of the site occupancy and detection estimates that have traditionally been associated with low-detection probabilities and heterogeneity in those probabilities. These findings confirm that the effects of availability may be important for ecologists and managers, and that where such effects are expected, modification of sampling designs and/or analytical methods should be considered. Failure to limit the effects of availability may preclude reliable estimation of the probability of site occupancy.

The Upper Mississippi River is thought to provide important stopover habitat for migrating landbirds because of its north-south orientation and floodplain forests. The river flows through the Driftless Area of southwestern Wisconsin and southeastern Minnesota where forests are plentiful, yet forests of the floodplain and Driftless Area uplands differ greatly in landscape setting, tree species composition, and topography. We compared landbird assemblages in these upland and floodplain forests over three springs, 2005–2007, using line-transect surveys at randomly selected areas in and within 16 km of the floodplain. We found more species of both transient and locally breeding migrants per survey in floodplain than in upland forest. Detections of transient neotropical migrants did not differ statistically by habitat. Detections of locally breeding neotropical and temperate-zone migrants and transient temperate-zone migrants were greater in floodplain than in upland forest. Between floodplain and up...

Occupancy models may be used to estimate the probability that a randomly selected site in an area of interest is occupied by a species (c), given imperfect detection (p). This method can be extended, given multiple survey periods, to permit the estimation of seasonal probabilities of c, colonization (g), persistence (w), and extinction (1 � w) in season t. We evaluated the sampling properties of estimators of these parameters using simulated data across a range of the parameters, differing levels of sites and visits, with a published dynamic occupancy model (Royle and Kery 2007). Bias depended largely on p and the number of visits, but also on the number of sites, ct, g, and 1 � w. To decrease bias in all parameters to near zero, our results suggest that the number of required visits will depend on p, such that the probability of detection at an occupied site is near 0.9, and the required number of sites will be near 60 for ct estimation and 120 or greater for g and 1 � w estimation. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.

The N-mixture model proposed by Royle in 2004 may be used to approximate the abundance and detection probability of animal species in a given region. In 2006, Royle and Dorazio discussed the advantages of using a Bayesian approach in modelling animal abundance and occurrence using a hierarchical N-mixture model. N-mixture models assume replication on sampling sites, an assumption that may be violated when the site is not closed to changes in abundance during the survey period or when nominal replicates are defined spatially. In this paper, we studied the robustness of a Bayesian approach to fitting the N-mixture model for pseudo-replicated count data. Our simulation results showed that the Bayesian estimates for abundance and detection probability are slightly biased when the actual detection probability is small and are sensitive to the presence of extra variability within local sites.

Contiguous floodplain lakes (‘lakes’) have historically been used as study units for comparative studies of limnological variables that vary within lakes. The hierarchical nature of these studies implies that study variables may be correlated within lakes and that covariate associations may differ not only among lakes but also by spatial scale. We evaluated the utility of treating lakes as study units for limnological variables that vary within lakes based on the criteria of important levels of among-lake variation in study variables and the observation of covariate associations that vary among lakes. These concerns were selected, respectively, to ensure that lake signatures were distinguishable from within-lake variation and that lake-scale effects on covariate associations might provide inferences not available by ignoring those effects. Study data represented chlorophyll a (CHL) and inorganic suspended solids (ISS) data from lakes within three reaches of the Upper Mississippi River. Sampling occurred in summer from 1993 through 2005 (except 2003); numbers of lakes per reach varied from 7 to 19, and median lake area varied from 53 to 101 ha. CHL and ISS levels were modelled linearly, with lake, year and lake × year effects treated as random. For all reaches, the proportions of variation in CHL and ISS attributable to differences among lakes (including lake and lake × year effects) were substantial (range: 18%–73%). Finally, among-lake variation in CHL and ISS was strongly associated with covariates and covariate effects that varied by lakes or lake-years (including with vegetation levels and, for CHL, log(ISS)). These findings demonstrate the utility of treating floodplain lakes as study units for the study of limnological variables and the importance of addressing hierarchy within study designs when making inferences from data collected within floodplain lakes. Published 2011. This article is a U.S. Government work and is in the public domain in the USA.

Estimation of site occupancy rates when detection probabilities are 300. We recommend applying site occupancy methods for monitoring presence of aquatic species.

Despite a heightened global concern for native mussels, fundamental research on mussel ecology in large rivers is lacking. These gaps in knowledge about where mussels occur, and why, are limiting habitat restoration activities. 2. Large-scale systematic surveys for native mussels in three reaches of the Upper Mississippi River documented mussel communities composed of 16-23 species and ranging from 2.9-4.5 live mussels m � 2 that were actively recruiting new cohorts into their populations (87-100% of the species were found as juveniles p5 years old). Estimates of mean tissue biomass and production in these reaches ranged from 2.1-3.1 g C m � 2 and 0.4-0.6 g C m � 2 year � 1 , respectively. 3. Mussels filtered a significant amount of water (range, 0.05-0.07 m 3 m � 2 d � 1 ) over a 480 km reach of the Upper Mississippi River - amounting to a filtration rate of 53.1 million m 3 day � 1 . The filtration rate of mussels as a percentage of river discharge ranged from 0.5-1.4% at high flows (5% exceedance), from 1.5-4.4% at moderate flows (50% exceedance) and from 4.4-12.2% during low flows (95% exceedance). 4. Collectively, these data suggest that native mussels play an integral role in this ecosystem by sequestering suspended materials that can be used by other benthic organisms. Published in 2011 by John Wiley and Sons, Ltd. Received 17 June 2010; Revised 20 December 2010; Accepted 21 December 2010

Reliable estimates of abundance are needed to assess consequences of proposed habitat restoration and enhancement projects on freshwater mussels in the Upper Mississippi River (UMR). Although there is general guidance on sampling techniques for population assessment of freshwater mussels, the actual performance of sampling designs can depend critically on the population density and spatial distribution at the project site. To evaluate various sampling designs, we simulated sampling of populations, which varied in density and degree of spatial clustering. Because of logistics and costs of large river sampling and spatial clustering of freshwater mussels, we focused on adaptive and non-adaptive versions of single and two-stage sampling. The candidate designs performed similarly in terms of precision (CV) and probability of species detection for fixed sample size. Both CV and species detection were determined largely by density, spatial distribution and sample size. However, designs did differ in the rate that occupied quadrats were encountered. Occupied units had a higher probability of selection using adaptive designs than conventional designs. We used two measures of cost: sample size (i.e. number of quadrats) and distance travelled between the quadrats. Adaptive and two-stage designs tended to reduce distance between sampling units, and thus performed better when distance travelled was considered. Based on the comparisons, we provide general recommendations on the sampling designs for the freshwater mussels in the UMR, and presumably other large rivers. Published in 2009 by John Wiley & Sons, Ltd.

Ecological restoration efforts in large rivers generally aim to ameliorate ecological effects associated with large-scale modification of those rivers. This study examined whether the effects of restoration efforts—specifically those of island construction—within a largely open water restoration area of the Upper Mississippi River (UMR) might be seen at the spatial scale of that 3476 ha area. The cumulative effects of island construction, when observed over multiple years, were postulated to have made the restoration area increasingly similar to a positive reference area (a proximate area comprising contiguous backwater areas) and increasingly different from two negative reference areas. The negative reference areas represented the Mississippi River main channel in an area proximate to the restoration area and an open water area in a related Mississippi River reach that has seen relatively little restoration effort. Inferences on the effects of restoration were made by comparing constrained and unconstrained models of summer chlorophyll a (CHL), summer inorganic suspended solids (ISS) and counts of benthic mayfly larvae. Constrained models forced trends in means or in both means and sampling variances to become, over time, increasingly similar to those in the positive reference area and increasingly dissimilar to those in the negative reference areas. Trends were estimated over 12- (mayflies) or 14-year sampling periods, and were evaluated using model information criteria. Based on these methods, restoration effects were observed for CHL and mayflies while evidence in favour of restoration effects on ISS was equivocal. These findings suggest that the cumulative effects of island building at relatively large spatial scales within large rivers may be estimated using data from large-scale surveillance monitoring programs. Published in 2010 by John Wiley & Sons, Ltd.

Royle and Link (Ecology 86(9):2505–2512, 2005) proposed an analytical method that allowed estimation of multinomial distribution parameters and classification probabilities from categorical data measured with error. While useful, we demonstrate algebraically and by simulations that this method yields biased multinomial parameter estimates when the probabilities of correct category classifications vary among sampling units. We address this shortcoming by treating these probabilities as logit-normal random variables within a Bayesian framework. We use Markov chain Monte Carlo to compute Bayes estimates from a simulated sample from the posterior distribution. Based on simulations, this elaborated Royle-Link model yields nearly unbiased estimates of multinomial and correct classification probability estimates when classification probabilities are allowed to vary according to the normal distribution on the logit scale or according to the Beta distribution. The method is illustrated using categorical submersed aquatic vegetation data.

Nesting belted kingfishers (hereafter kingfishers, Ceryle alcyon) were studied on the Hudson River near Fort Edward south to New Baltimore (NY, USA) and three nearby river drainages in 2004. Concentrations of 28 organochlorine pesticides, 160 polychlorinated biphenyl (PCB) congeners, and 17 dioxin and furan (PCDD-F) congeners were quantified in kingfisher eggs. The pattern of organochlorine pesticides and PCDD-F congeners did not differ significantly between 14 eggs collected from individual nests on the Hudson River and five eggs similarly collected on three other nearby rivers. In contrast, the pattern of PCB congeners in eggs collected on the Hudson River differed significantly from the other rivers. The differences in patterns of PCB congeners were associated with a higher representation of lower-numbered congeners on the Hudson River than the other rivers. The higher prevalence of the lower-numbered congeners and lower prevalence of the higher-numbered congeners is consistent with Aroclor 1016 and 1242 being the source of the PCBs on the Hudson River. Concentrations in a sample egg collected at each nest were compared to nest survival and egg success (the proportion of eggs hatching in a clutch if at least one egg hatched) of the remaining eggs in the clutch. Models that predicted nest survival and egg success as functions of contaminant levels were poorly distinguished from models that presumed no such associations. Small sample sizes could have contributed to the inability to distinguish among contaminant and no toxicant models. However, we cannot rule out the possibility that contaminant concentrations on the Hudson River were not sufficiently high to demonstrate a relationship between contaminant concentrations and reproductive success in kingfishers. Environ. Toxicol. Chem. 2010;29:99–110. Published 2009 SETAC

In 2004, spotted sandpipers (Actitis macularia) were studied on the Hudson River near Fort Edward south to New Baltimore, NY and on two river drainages that flow into the Hudson River. Concentrations of 28 organochlorine pesticides, 160 polychlorinated biphenyl (PCB) congeners, and 17 dioxin and furan (PCDD-F) congeners were quantified in eggs collected on and off the Hudson River. The pattern of organochlorine pesticides and PCDD-F congeners did not differ significantly between eggs collected on and off the Hudson River. In contrast, the pattern of PCB congeners differed significantly between the Hudson River and other rivers. Total PCBs were significantly greater in eggs from the Hudson River (geometric mean = 9.1 microg PCBs/g wet weight) than from the other two rivers (0.6 and 0.6 microg PCBs/g wet weight). Seven of 35 (20%) eggs exceeded 20 microg PCBs/g wet weight, the estimated threshold for reduced hatching in tree swallows (Tachycineta bicolor) and some raptor species; the maximum concentration was 72.3 microg PCBs/g wet weight. Models that predicted nest survival and egg success (the proportion of eggs hatching in a clutch if at least one egg hatched) as functions of contaminant levels were poorly distinguished from models that presumed no such associations. While small sample size could have contributed to the inability to distinguish among contaminant and no toxicant models, we cannot rule out the possibility that contaminant concentrations on the Hudson River were not sufficiently high to demonstrate a relationship between contaminant concentrations and reproductive success.

Multilevel models are used to model processes associated with hierarchical data structures. Despite infrequent use in the biological and environmental sciences, the use of these models with hierarchically-structured data conveys multiple advantages. These include the assessment of whether covariate effects differ among groups or clusters, and separate estimation of covariate effects by hierarchical level (thereby addressing atomistic and aggregation fallacy concerns). We illustrate these advantages using larval mayfly count data derived from annual surveys on the Mississippi River and a continuous covariate (water depth).

Partitioning the variance of a response by design levels is challenging for binomial and other discrete outcomes. Goldstein (2003) proposed four definitions for variance partitioning coefficients (VPC) under a two-level logistic regression model. In this study, we explicitly derived formulae for multi-level logistic regression model and subsequently studied the distributional properties of the calculated VPCs. Using simulations and a vegetation dataset, we demonstrated associations between different VPC definitions, the importance of methods for estimating VPCs (by comparing VPC obtained using Laplace and penalized quasilikehood methods), and bivariate dependence between VPCs calculated at different levels. Such an empirical study lends an immediate support to wider applications of VPC in scientific data analysis.

Impounding large rivers has often led to reductions in aquatic habitat diversity over time. One approach used to restore habitat on the Upper Mississippi River is island construction. A specific purpose of island construction is to increase the growth and diversity of aquatic macrophytes. We addressed whether this purpose was met for islands constructed in a reach of the Upper Mississippi River. Aquatic macrophyte levels and richness around 2 constructed island complexes were compared with those in open water reference areas in 1998 and 2000. These data suggest that macrophyte levels increased in the construction area relative to the reference area for the second but not the first island complex. Findings were similar for both percent frequency of occurrence and richness index models. These differences in response are attributed to the differing maturities of the 2 island complexes. The first complex was completed 6 years prior to the initiation of aquatic macrophyte sampling, whereas sampling be...

Invasive plants are a growing concern worldwide for conservation of native habitats. In endangered wet meadow habitat in the Upper Midwestern United States, reed canary grass (Phalaris arundinacea) is a recognized problem and its prevalence is more widespread than the better-known invasive wetland plant purple loosestrife (Lythrum salicaria). Although resource managers are concerned about the effect of reed canary grass on birds, this is the first study to report how common wet meadow birds use habitat in relation to reed canary grass cover and dominance. We examined three response variables: territory placement, size of territories, and numbers of territories per plot in relation to cover of reed canary grass. Territory locations for Sedge Wren (Cistothorus platensis) and Song Sparrow (Melospiza melodid) were positively associated with reed canary grass cover, while those for Common Yellowthroat (Geothlypis trichas) were not. Only Swamp Sparrow (M. georgiana) territory locations were negatively associated with reed canary grass cover and dominance (which indicated a tendency to place territories where there was no reed canary grass or where many plant species occurred with reed canary grass). Swamp Sparrow territories were positively associated with vegetation height density and litter depth. Common Yellowthroat territories were positively associated with vegetation height density and shrub cover. Song Sparrow territories were negatively associated with litter depth. Reed canary grass cover within territories was not associated with territory size for any of these four bird species. Territory density per plot was not associated with average reed canary grass cover of plots for all four species. Sedge Wrens and Song Sparrows may not respond negatively to reed canary grass because this grass is native to wet meadows of North America, and in the study area it merely replaces other tall lush plants. Avoidance of reed canary grass by Swamp Sparrows may be mediated through their preference for wet areas where reed canary grass typically does not dominate.

Environmental scientists face multiple challenges when analyzing unevenly recorded time series with small sample sizes. For example, trends in water temperature may be confounded with time and date of sampling when the latter represent convenience samples and thus introduce bias into regression estimates. We address these concerns using multilevel random slope models and nonparametric bootstrap inference for assessing the statistical significance of the annual trend in river temperature when measurement times and dates are haphazard.

The selection of a distributional assumption suitable for modelling macroinvertebrate density data is typically challenging. Macroinvertebrate data often exhibit substantially larger variances than expected under a standard count assumption, that of the Poisson distribution. Such overdispersion may derive from multiple sources, including heterogeneity of habitat (historically and spatially), differing life histories for organisms collected within a single collection in space and time, and autocorrelation. Taken to extreme, heterogeneity of habitat may be argued to explain the frequent large proportions of zero observations in macroinvertebrate data. Sampling locations may consist of habitats defined qualitatively as either suitable or unsuitable. The former category may yield random or stochastic zeroes and the latter structural zeroes. Heterogeneity among counts may be accommodated by treating the count mean itself as a random variable, while extra zeroes may be accommodated using zero-modified count assumptions, including zero-inflated and two-stage (or hurdle) approaches. These and linear assumptions (following log- and square root-transformations) were evaluated using 9 years of mayfly density data from a 52 km, ninth-order reach of the Upper Mississippi River (n = 959). The data exhibited substantial overdispersion relative to that expected under a Poisson assumption (i.e. variance:mean ratio = 23 ≫ 1), and 43% of the sampling locations yielded zero mayflies. Based on the Akaike Information Criterion (AIC), count models were improved most by treating the count mean as a random variable (via a Poisson-gamma distributional assumption) and secondarily by zero modification (i.e. improvements in AIC values = 9184 units and 47–48 units, respectively). Zeroes were underestimated by the Poisson, log-transform and square root-transform models, slightly by the standard negative binomial model but not by the zero-modified models (61%, 24%, 32%, 7%, and 0%, respectively). However, the zero-modified Poisson models underestimated small counts (1 ≤ y ≤ 4) and overestimated intermediate counts (7 ≤ y ≤ 23). Counts greater than zero were estimated well by zero-modified negative binomial models, while counts greater than one were also estimated well by the standard negative binomial model. Based on AIC and percent zero estimation criteria, the two-stage and zero-inflated models performed similarly. The above inferences were largely confirmed when the models were used to predict values from a separate, evaluation data set (n = 110). An exception was that, using the evaluation data set, the standard negative binomial model appeared superior to its zero-modified counterparts using the AIC (but not percent zero criteria). This and other evidence suggest that a negative binomial distributional assumption should be routinely considered when modelling benthic macroinvertebrate data from low flow environments. Whether negative binomial models should themselves be routinely examined for extra zeroes requires, from a statistical perspective, more investigation. However, this question may best be answered by ecological arguments that may be specific to the sampled species and locations.

The effect of drying conditions on harpagoside (HS) retention, as well as the use of near-infrared spectroscopy (NIRS) for rapid quantification of the iridoids, HS, and 8-rho-coumaroyl harpagide (8rhoCHG) and moisture, in dried Harpagophytum procumbens (devil's claw) root was investigated. HS retention was significantly (P < 0.05) lower in sun-dried samples as compared to tunnel-dried (60 degrees C, 30% relative humidity) and freeze-dried samples. The best retention of HS was obtained at 50 degrees C when evaluating tunnel drying at dry bulb temperatures of 40, 50, and 60 degrees C and 30% relative humidity. NIRS can effectively predict moisture content with a standard error of prediction (SEP) and correlation coefficient (r) of 0.24% and 0.99, respectively. The HS and 8rhoCHG NIRS calibration models established for both iridoid glucosides can be used for screening purposes to get a semiquantitative classification of devil's claw roots (for HS: SEP = 0.236%, r = 0.64; for 8rhoCHG: SEP = 0.048%, r = 0.73).

SUMMARY 1. Macroinvertebrate count data often exhibit nested or hierarchical structure. Examples include multiple measurements along each of a set of streams, and multiple synoptic measurements from each of a set of ponds. With data exhibiting hierarchical structure, outcomes at both sampling (e.g. within stream) and aggregated (e.g. stream) scales are often of interest. Unfortunately, methods for modelling hierarchical count data have received little attention in the ecological literature. 2. We demonstrate the use of hierarchical count models using fingernail clam (Family: Sphaeriidae) count data and habitat predictors derived from sampling and aggregated spatial scales. The sampling scale corresponded to that of a standard Ponar grab (0.052 m 2 ) and the aggregated scale to impounded and backwater regions within 38–197 km reaches of the Upper Mississippi River. Impounded and backwater regions were resampled annually for 10 years. Consequently, measurements on clams were nested within years. Counts were treated as negative binomial random variates, and means from each resampling event as random departures from the impounded and backwater region grand means. 3. Clam models were improved by the addition of covariates that varied at both the sampling and regional scales. Substrate composition varied at the sampling scale and was associated with model improvements, and reductions (for a given mean) in variance at the sampling scale. Inorganic suspended solids (ISS) levels, measured in the summer preceding sampling, also yielded model improvements and were associated with reductions in variances at the regional rather than sampling scales. ISS levels were negatively associated with mean clam counts. 4. Hierarchical models allow hierarchically structured data to be modelled without ignoring information specific to levels of the hierarchy. In addition, information at each hierarchical level may be modelled as functions of covariates that themselves vary by and within levels. As a result, hierarchical models provide researchers and resource managers with a method for modelling hierarchical data that explicitly recognises both the sampling design and the information contained in the corresponding data.

In some agricultural regions, natural wetlands are scarce, and constructed agricultural ponds may represent important alternative breeding habitats for amphibians. Properly managed, these agricultural ponds may effectively increase the total amount of breeding habitat and help to sustain populations. We studied small, constructed agricultural ponds in southeastern Minnesota to assess their value as amphibian breeding sites. Our study examined habitat factors associated with amphibian reproduction at two spatial scales: the pond and the landscape surrounding the pond. We found that small agricultural ponds in southeastern Minnesota provided breeding habitat for at least 10 species of amphibians. Species richness and multispecies reproductive success were more closely associated with characteristics of the pond (water quality, vegetation, and predators) compared with char- acteristics of the surrounding landscape, but individual species were associated with both pond and landscape variables. Ponds surrounded by row crops had similar species richness and reproductive success compared with natural wetlands and ponds surrounded by non- grazed pasture. Ponds used for watering livestock had elevated concentrations of phos- phorus, higher turbidity, and a trend toward reduced amphibian reproductive success. Spe- cies richness was highest in small ponds, ponds with lower total nitrogen concentrations, tiger salamanders ( Ambystoma tigrinum) present, and lacking fish. Multispecies reproduc- tive success was best in ponds with lower total nitrogen concentrations, less emergent vegetation, and lacking fish. Habitat factors associated with higher reproductive success varied among individual species. We conclude that small, constructed farm ponds, properly managed, may help sustain amphibian populations in landscapes where natural wetland habitat is rare. We recommend management actions such as limiting livestock access to the pond to improve water quality, reducing nitrogen input, and avoiding the introduction of fish.

Procedurally defined periphyton frequently includes substantial quantities of hydrous iron (Fe) and manganese (Mn) oxides. As these oxides are strong sorbers of heavy metals, their presence may complicate estimation of metal bioaccumulation by periphyton. We examined the relationship between nickel (Ni) sorption and the development time, biomass, and Fe and Mn oxide content of stream periphyton. Development time, the time during which periphyton accrued on submerged tile substrata, was used to provide variation in biomass, Fe and Mn levels. Stream periphyton from four development times was exposed to Ni for 2 h in the laboratory, and then ashed. Development time was significantly associated with ash-free dry mass (AFDM), Fe and Mn levels (ANOVA, P ⩽0.003). Ni extracted by a mild reductant (hydroxylamine hydrochloride) was significantly associated with development time, and with AFDM, Fe and Mn levels (linear models, P ⩽0.0002). A subsequent acid digestion yielded similar associations with the same variables (linear models, P ⩽0.0001). For both extractions, AFDM was significantly and positively correlated with Fe ( r =0.68 and 0.89) and with Mn ( r =0.77 and 0.93) (Spearman rank, P ⩽0.005). These data demonstrate the importance of periphyton development time in influencing both metal sorption and levels of biomass and ferromanganese oxides. The data also suggest that metal contaminant levels in periphyton should not be attributed automatically to biotic sorption. Periphyton metal-accumulation studies conducted where ferromanganese oxide concentrations are elevated should address the potential metal-sorbing roles of Fe and Mn oxides within the periphyton matrix.

This article describes the selection process used to identify optimal measures of growth and reproduction for the proposed 28-d sublethal sediment bioassay with the estuarine amphipod Leptocheirus plumulosus. The authors used four criteria (relevance of each measure to its respective endpoint, signal-to-noise ratio, redundancy relative to other measures of the same endpoint, and cost) to evaluate nine growth and seven reproductive measures. Optimal endpoint measures were identified as those receiving relatively high scores for all or most criteria. Measures of growth scored similarly on all criteria, except for cost. The cost of the pooled (female plus male) growth measures was substantially lower than the cost of the female and male growth measures because the latter required more labor (by approx. 25 min per replicate). Pooled dry weight was identified as the optimal growth measure over pooled length because the latter required additional labor and nonstandard software and equipment. Embryo and neonate measures of reproduction exhibited wide differences in labor costs but yielded similar scores for other criteria. In contrast, brooding measures of reproduction scored relatively low on endpoint relevance, signal-to-noise ratio, and redundancy criteria. The authors recommend neonates/survivor as the optimal measure of L. plumulosus reproduction because it exhibited highmore » endpoint relevance and signal-to-noise ratios, was redundant to other reproductive measures, and required minimal time.« less

Based on the need for a test to evaluate chronic sublethal toxicity in estuarine sediments, a 28-d sediment bioassay with the estuarine amphipod Leptocheirus plumulosus (Shoemaker) was developed. The test was initiated with animals less than 2 weeks old (i.e., 425–600 μm sieved size class). Test endpoints included survival, growth (μg dry weight/d), and reproduction (number of neonates/surviving female). Factors with the potential to influence test animal performance (i.e., nontreatment factors) such as artificial sea salts, salinity, food ration, size at test initiation, intraspecific density, sediment grain size, and diet were evaluated. For example, intraspecific densities between 10 and 60 animals/beaker (i.e., 0.18–1.4 animals/cm2) did not affect survival, growth, or reproduction. Similarly, L. plumulosus were tolerant of a wide range of sediment grain sizes with only extremely fine grained (e.g., >75% clay) or coarse grained (e.g., >75% sand) material significantly affecting survival, growth, and reproduction. Test performance criteria included control survival (>80%) and reproduction (production of offspring in all control replicates), and response to a reference toxicant test with cadmium chloride in a control chart format.

High levels of ammonia in sediment toxicity tests can potentially confound test results. At issue is whether the observed toxicity is due to elevated ammonia or the presence of more persistent anthropogenic contaminants. To evaluate the risk of ammonia toxicity, information on (1) the exposure–response relationship and (2) the probability of exposure are needed. Preliminary exposure–response data were obtained for two different sieved size classes of the estuarine amphipod Leptocheirus plumulosus representing juveniles (425–600 μm) and subadults (not reproductively active) (600–1,000 μm) in 4-d water-only exposures with ammonia (NH4Cl). Resulting LC50 values were 44 (juvenile) and 89 mg NH3-N/L (subadult). Results from 4-d tests were used to establish exposure concentrations for two spiked-sediment studies: (1) a 10-d static exposure starting with subadults measuring survival and growth and (2) a 28-d exposure with daily renewal of overlying water starting with juveniles and measuring survival, growth, and reproduction. Risk of ammonia toxicity to L. plumulosus during sediment toxicity tests was characterized via a Monte Carlo simulation using the exposure–response curves from laboratory spiked-sediment studies and published porewater ammonia values for 322 marine sediments. Results indicate a significant potential for ammonia induced interference in the 10-d test (e.g., 2–18% probability of significant mortality due to ammonia alone). Risk in 28-d tests appears to be minimal due to rapid dissipation of ammonia via renewal of overlying water.

Seventeen Great Lakes sediments ranging in degree of expected toxicity were evaluated using a 21 day sediment elutriate bioassay with Daphnia magna. Sediments differed in their effects on survival, age at first reproduction, the number of broods produced and the total number of young produced per adult. Sediments producing low survivorship (50-60%) also had negative effects on reproduction. However, both positive and negative effects on reproduction were found among sediments producing high survivorship. To integrate all test end-points, a stochastic matrix population model was constructed and parameterized with survival and reproduction data from each sediment. By including estimates of variability in vital rates, the model output provided quantitative estimates of uncertainty in projected population size. Sediment effects on survival and reproduction translated into large differences in projected population growth; mean estimates of projected population size at day 28 of the simulations ranged over two orders of magnitude among the 17 sediments. Reproductive timing (e.g. age at first reproduction), followed by fecundity and survivorship, had the largest effect on population growth. Results of this study also indicate that the presence of suspended sediment in elutriates may confound toxicity evaluations using cladocerans. The concentration of total suspended solids was negatively correlated with age at first reproduction and positively correlated with measures of fecundity and population growth. In order to realize the potential benefits of chronic testing we must develop ecologically relevant ways of interpreting sediment bioassay results and expressing the uncertainty associated with our estimates of ecological risk.

Photosynthetic activity and nickel sorption by stream periphyton were examined in relation to light intensity. Ceramic tiles supporting moderate levels of periphyton were placed in laboratory microcosms and exposed to nickel ion and 14 C-labeled sodium bicarbonate. Sorption of nickel increased hyperbolically as light intensity increased from zero to 300 μmol quanta m -2 s -1 ; this response was similar to the photosynthesis-irradiance relationship for periphyton collected from the same site. Nickel sorption with light was up to 76% greater than nickel sorption in the dark. Dark-related nickel sorption was likely attributable to sorption by hydrous iron and manganese oxides and to passive biotic sorption. These results suggest an important relationship between nickel sorption and photosynthesis, which may be a result of active uptake, adsorption through cation exchange, or nickel precipitation.

emphasis on cross-classified sampling designs. In Gitzen R.A., J.J. Millspaugh, A.B. Cooper, and D.S. Licht, Design and Analysis of Long-term Ecological Monitoring Studies. Cambridge University Press, pp. 200-227. VARIANCE COMPONENTS ESTIMATION FOR CONTINUOUS AND DISCRETE DATA, WITH EMPHASIS ON CROSS-CLASSIFIED SAMPLING DESIGNS Brian R. Gray Upper Midwest Environmental Sciences Center, U.S. Geological Survey, La Crosse, WI 54603 USA

To determine the level of in ovo methylmercury (MeHg) exposure that results in detrimental effects on fitness and survival of loon embryos and hatched chicks, we conducted a field study in which we injected eggs with various doses of MeHg on day 4 of incubation. Eggs were collected following about 23 days of natural incubation and artificially incubated to observe hatching. Reduced embryo survival was evident in eggs injected at a rate of ≥1.3 μg Hg/g wet-mass. When maternally deposited Hg and injected Hg were considered together, the median lethal concentration of Hg (LC(50)) was estimated to be 1.78 μg Hg/g wet-mass. Organ mass patterns from eggs of chicks injected at a rate of 2.9 μg Hg/g differed from that of controls and chicks from the 0.5 μg Hg/g treatment, largely related to a negative relation between yolk sac mass and egg mercury concentration. Chicks from eggs in the 2.9 μg Hg/g treatment were also less responsive to a frightening stimulus than controls and chicks from the 0.5 μg Hg/g treatment. We also found that the length of incubation period increased with increasing egg mercury concentration. Tissue Hg concentrations were strongly associated (r(2) ≥ 0.80) with egg Hg concentration.

The laying order of tree swallow eggs was identified from the Housatonic River, Berkshire County, Massachusetts, USA, and eggs were chemically analyzed individually to document possible effects of laying order on organic contaminant and inorganic element concentrations. Effects of laying order on other parameters such as egg weight, size, and lipid and moisture content also were assessed. Some effects of egg order on total polychlorinated biphenyls (PCBs) were detected, but the effect was not uniform across individual females or between years. In 2004, clutches with higher total PCBs tended to have concentrations decline across egg order, whereas clutches with lower concentrations of PCBs tended to increase across egg order. In contrast, in 2005, there was a tendency for concentrations to increase across egg order. Polychlorinated biphenyl concentrations were highly variable within and among clutches in both years. The directionality of egg order associations (i.e., slopes) for trace elements was element dependent, was positive for Mn and Zn, was negative for B, and had no slope for Cr. Whole egg weight increased across egg order. Percentage lipid was variable within a clutch, with no pattern common across all females. Percentage lipid was also correlated with organic contaminant concentration. In highly contaminated environments, higher lipid content could have the unanticipated corollary of having higher concentrations of lipophilic contaminants such as PCBs. To reduce the effect of high variation within a clutch when assessing contamination exposure, it is recommended that two eggs per clutch be collected and pooled for chemical analysis. We further recommend that, as long as the two eggs are randomly collected, the additional effort needed to identify and collect specific eggs is not warranted. Environ. Toxicol. Chem. 2010;29:909–921. © 2009 SETAC