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Geology topics

Brian R. Gray

Publications and source records attributed to Brian R. Gray.

At least 37 records · Page 2Linked to original sources
USGS2018

Separable correlation and maximum likelihood

We consider estimation of the covariance matrix of a multivariate normal distribution when the correlation matrix is separable in the sense that it factors as a Kronecker product of two smaller matrices. A computationally convenient coordinate descent-type algorithm is developed for maximum likelihood estimation. Simulations indicate our method often gives smaller estimation error than some common alternatives when correlation is separable, and that correctly sized tests for correlation separability can be obtained using a parametric bootstrap. Using dissolved oxygen data from the Upper Mississippi River, we illustrate how our model can lead to interesting scientific findings that may be missed when using competing models.

arXiv↗
USGS2017

Differences in breeding bird assemblages related to reed canary grass cover cover and forest structure on the Upper Mississippi River

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 ,15%, resulting from prolonged spring flooding. These sites hosted more prothonotary warbler Protonotaria citrea , but they had reduced bird abundance and diversity compared to other sites. Our results indicate that frequently flooded sites may be important for prothonotary warblers and that bird assemblages shift in response to reed canary grass invasion.

Upper Mississippi River↗
USGS2017

Estimating linear temporal trends from aggregated environmental monitoring data

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.

Ecological Indicators↗
USGS2017

Lethal and sub-lethal responses of native freshwater mussels exposed to granular Bayluscide®, a sea lamprey larvicide

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.

Journal of Great Lakes Research↗
USGS2015

Estimation of river and stream temperature trends under haphazard sampling

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.

Illinois River↗
USGS2015

Influence of in ovo mercury exposure, lake acidity, and other factors on common loon egg and chick quality in Wisconsin

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 mg/g to 1.23mg/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 0.84ug/g to 3.86 ug/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.

Wisconsin↗
USGS2015

Host–parasite behavioral interactions in a recently introduced, whooping crane population

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.

Wisconsin↗
USGS2014

Mortality, movement and behaviour of native mussels during a planned water-level drawdown in the Upper Mississippi River

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.

Minnesota, Wisconsin↗
USGS2014

Can mercury in fish be reduced by water level management? Evaluating the effects of water level fluctuation on mercury accumulation in yellow perch ( Perca flavescens )

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.

Ecotoxicology↗
USGS2013

Influences of Availability on Parameter Estimates from Site Occupancy Models with Application to Submersed Aquatic Vegetation

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.

Natural Resource Modeling↗
USGS2013

Nutrient cycling, connectivity, and free-floating plant abundance in backwater lakes of the Upper Mississippi River

River eutrophication may cause the formation of dense surface mats of free floating plants (FFP; e.g., duckweeds and filamentous algae) which may adversely affect the ecosystem. We investigated associations among hydraulic connectivity to the channel, nutrient cycling, FFP, submersed aquatic vegetation (SAV), and dissolved oxygen concentration (DO) in ten backwater lakes of the Upper Mississippi River (UMR) that varied in connectivity to the channel. Greater connectivity was associated with higher water column nitrate (NO3-N) concentration, higher rates of sediment phosphorus (P) release, and higher rates of NO3-N flux to the sediments. Rates of sediment P and N (as NH4-N) release were similar to those of eutrophic lakes. Water column nutrient concentrations were high, and FFP tissue was nutrient rich suggesting that the eutrophic condition of the UMR often facilitated abundant FFP. However, tissue nutrient concentrations, and the associations between FFP biomass and water column nutrient concentrations, suggested that nutrients constrained FFP abundance at some sites. FFP abundance was positively associated with SAV abundance and negatively associated with dissolved oxygen concentration. These results illustrate important connections among hydraulic connectivity, nutrient cycling, FFP, SAV, and DO in the backwaters of a large, floodplain river.

Upper Mississippi River↗
USGS2013

Songbird use of floodplain and upland forests along the Upper Mississippi River corridor during spring migration

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 upland forest, assemblages of locally breeding species, including neotropical and temperate-zone migrants (of which some individuals were in transit), differed substantially, but assemblages of transients (including both neotropical and temperate-zone migrants) did not differ as much. Only two species of transient migrants had clear affinities for floodplain forest, and none had an affinity for upland forest, whereas most locally breeding migrants had an affinity for either upland or floodplain forest. Within each spring, however, detections of transient neotropical migrants shifted from being greater in floodplain to greater in upland forests. This intraseasonal shift may be related to the phenology of certain tree species.

Iowa;Minnesota;Wisconsin↗
USGS2012

Variance components estimation for continuous and discrete data, with emphasis on cross-classified sampling designs

Variance components may play multiple roles (cf. Cox and Solomon 2003). First, magnitudes and relative magnitudes of the variances of random factors may have important scientific and management value in their own right. For example, variation in levels of invasive vegetation among and within lakes may suggest causal agents that operate at both spatial scales – a finding that may be important for scientific and management reasons. Second, variance components may also be of interest when they affect precision of means and covariate coefficients. For example, variation in the effect of water depth on the probability of aquatic plant presence in a study of multiple lakes may vary by lake. This variation will affect the precision of the average depth-presence association. Third, variance component estimates may be used when designing studies, including monitoring programs. For example, to estimate the numbers of years and of samples per year required to meet long-term monitoring goals, investigators need estimates of within and among-year variances. Other chapters in this volume (Chapters 7, 8, and 10) as well as extensive external literature outline a framework for applying estimates of variance components to the design of monitoring efforts. For example, a series of papers with an ecological monitoring theme examined the relative importance of multiple sources of variation, including variation in means among sites, years, and site-years, for the purposes of temporal trend detection and estimation (Larsen et al. 2004, and references therein).

Book chapter↗
USGS2011

Effects of injected methylmercury on the hatching of common loon (Gavia immer) eggs

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.

Wisconsin↗
USGS2011

Population assessment and potential functional roles of native mussels in the Upper Mississippi River

1. 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 5 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.

Illinois, Iowa, Minnesota, Missouri, Wisconsin↗
USGS2010

Multinomial mixture model with heterogeneous classification probabilities

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.

Environmental and Ecological Statistics↗
USGS2010

Polychlorinated biphenyls, dioxins, furans, and organochlorine pesticides in belted kingfisher eggs from the upper Hudson River basin, New York, USA

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.

New York↗