Modeling misidentification errors that result from use of genetic tags in capture–recapture studies

Misidentification of animals is potentially important when naturally existing features (natural tags) such as DNA fingerprints (genetic tags) are used to identify individual animals. For example, when misidentification leads to multiple identities being assigned to an animal, traditional estimators tend to overestimate population size. Accounting for misidentification in capture–recapture models requires detailed understanding of the mechanism. Using genetic tags as an example, we outline a framework for modeling the effect of misidentification in closed population studies when individual identification is based on natural tags that are consistent over time (non-evolving natural tags). We first assume a single sample is obtained per animal for each capture event, and then generalize to the case where multiple samples (such as hair or scat samples) are collected per animal per capture occasion. We introduce methods for estimating population size and, using a simulation study, we show that our new estimators perform well for cases with moderately high capture probabilities or high misidentification rates. In contrast, conventional estimators can seriously overestimate population size when errors due to misidentification are ignored.     

Seasonal Flushing of Pollutant Concentrations and Loads in Urban Stormwater1

Schiff, Kenneth C. and Liesl L. Tiefenthaler, 2011. Seasonal Flushing of Pollutant Concentrations and Loads in Urban Stormwater. Journal of the American Water Resources Association (JAWRA) 47(1):136‐142. DOI: 10.1111/j.1752‐1688.2010.00497.x Abstract: Despite broad observations of first flush within storms, the scientific understanding of seasonal flushing remains incomplete. Seasonal flushing occurs when initial storms of the season have greater concentrations or loads than storms later in the season. The goal of this study was to census stormwater concentrations and loads from an arid, urban watershed to quantify seasonal flushing. Samples were collected every 15 min during the 1997‐1998 wet season from the Santa Ana River and analyzed for total suspended solids. Initial storms of the season generated event mean concentrations 3‐10 times the event mean concentration of storms later in the season. Cumulative flow‐weighted mean concentrations were calculated as the season progressed. Early season storms discharged only 6% of the annual volume, but influenced flow‐weighted mean concentrations well past the midpoint of the wet season. Mass‐based estimates also indicated a disproportionate load in the early portion of the year; over 52% of the annual load was discharged in the first 30% of the annual volume from the highly urbanized lower watershed. Other stormwater pollutants, including six trace metals (Cd, Cr, Cu, Pb, Ni, Zn), were highly correlated with total suspended solids and also exhibited a significant seasonal flush.     

Avoidance and toxicity responses of fish to intermittent chlorination

The ability of fish to actively avoid concentrations of chlorine in a steep, horizontal, laboratory-controlled gradient was found to be species-specific and dependent upon the acclimation temperature, water quality conditions, and the type of chlorine residual tested. Comparison of behavioral avoidances with the results from bioassays using some form of intermittent chlorination, as reported in the literature, indicated that LC₅₀ concentrations (levels that cause the mortality of half the test individuals in a designated time period) usually exceeded avoidance threshold concentrations.This chlorine avoidance study, which was carried out in a field laboratory that utilized New River water for holding and testing procedures, was located at the Glen Lyn power plant in southwestern Virginia. Two basic types of avoidance trials were employed, TRC (total residual chlorine) and chloramine (CRC) exposures. The TRC trials contained variable amounts of free (FRC) and combined residual chlorine (CRC) depending upon water quality, while in chloramine trials, the TRC exposure was mainly comprised of monochloramine with little or no FRC. The first significant avoidance in TRC trials for several fish species tested, varied from 0.05 mg/1 for coho salmon (Oncorhynchus kisutch) to 0.40 for channel catfish (Ictalurus punctatus). Low levels of hypochlorous acid (HOCl), which are considered to be a potentially toxic constituent of FRC, appeared to consistently influence the avoidance response. Initial avoidance concentrations to HOCl ranged from 0.01–0.02 mg/1 for coho salmon to 0.04–0.12 mg/1 for channel catfish, depending upon acclimation temperatures tested. The pH in river water was more influential than temperature in controlling the amount of HOCl present within the FRC at each TRC exposure. Avoidance responses by fish to CRC concentrations were either equal to or greater than TRC exposures and were dependent upon the ammonia-N content. Chloramine and FRC (specifically the HOCl fraction) have been reported to have different mechanisms of toxicity, which offered possible explanations for the differences observed in avoidance behavior. Chlorine residuals discharged from the Glen Lyn power plant in previous years have exceeded the LC₅₀ values reported for many species, although no major fish kills from chlorine have been documented. Behavioral avoidance responses by fish to potentially lethal chlorinated discharges in aquatic receiving systems may be a major mechanism of these populations in adapting to or interacting within these industrially influenced environments.     

Response of antibiotics and resistance genes to high-intensity and low-intensity manure management

The purpose of this study was to determine the response of antibiotics and antibiotic resistance genes (ARG) to manure management. A pilot field study was conducted using horse manure containing no antibiotics, into which chlortetracycline (CTC), tylosin (TYL), and monensin (MON) were spiked and compared to unspiked controls. Subsequently, a large-scale field study was conducted comparing manure from a dairy with minimal use of antibiotics and a feedlot with regular subtherapeutic use of antibiotics. The manures were subjected to high-intensity management (HIM) (amending, watering, and turning) and low-intensity management (LIM) (no amending, watering, or turning) and were monitored for antibiotic concentrations and levels of tetracycline ARG [tet(W) and tet(O)] using quantitative real-time polymerase chain reaction. All three antibiotics in the pilot study dissipated more rapidly in HIM manure, with half-lives ranging from 4 to 15 d, compared to LIM manure, with half-lives ranging from 8 to 30 d. Levels of tet(W) were significantly higher after 141 d of treatment, but levels of tet(O) were significantly lower in all treatments. In the large-scale study, the feedlot manure had higher initial concentrations than the dairy manure of tetracycline (TC), oxytetracycline (OTC), and CTC as well as tet(W) and tet(O). Tetracycline and OTC dissipated more rapidly in HIM manure, with half-lives ranging from 6 to 15 d, compared to LIM manure, with half-lives ranging from 7 to 31 d. After 6 mo of treatment, tet(W) and tet(O) decreased significantly in feedlot manure, whereas dairy manure required only 4 mo of treatment for similar results.     

Comparison of plant families in a greenhouse phytoremediation study on an aged polycyclic aromatic hydrocarbon-contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous, recalcitrant, and potentially carcinogenic pollutants. Plants and their associated rhizosphere microbes can promote PAH dissipation, offering an economic and ecologically attractive remediation technique. This study focused on the effects of different types of vegetation on PAH removal and on the interaction between the plants and their associated microorganisms. Aged PAH-polluted soil with a total PAH level of 753 mg kg(-1) soil dry weight was planted with 18 plant species representing eight families. The levels of 17 soil PAHs were monitored over 14 mo. The size of soil microbial populations of PAH degraders was also monitored. Planting significantly enhanced the dissipation rates of all PAHs within the first 7 mo, but this effect was not significant after 14 mo. Although the extent of removal of lower-molecular-weight PAHs was similar for planted and unplanted control soils after 14 mo, the total mass of five- and six-ring PAHs removed was significantly greater in planted soils at the 7- and 14-mo sampling points. Poaceae (grasses) were the most effective of the families tested, and perennial ryegrass was the most effective species; after 14 mo, soils planted with perennial ryegrass contained 30% of the initial total PAH concentration (compared with 51% of the initial concentrations in unplanted control soil). Although the presence of some plant species led to higher populations of PAH degraders, there was no correlation across plant species between PAH dissipation and the size of the PAH-degrading population. Research is needed to understand differences among plant families for stimulating PAH dissipation.     

Spatiotemporal variation in survival rates: implications for population dynamics of yellow-bellied marmots

Spatiotemporal variation in age-specific survival rates can profoundly influence population dynamics, but few studies of vertebrates have thoroughly investigated both spatial and temporal variability in age-specific survival rates. We used 28 years (1976-2003) of capture-mark-recapture (CMR) data from 17 locations to parameterize an age-structured Cormack-Jolly-Seber model, and investigated spatial and temporal variation in age-specific annual survival rates of yellow-bellied marmots (Marmota flaviventris). Survival rates varied both spatially and temporally, with survival of younger animals exhibiting the highest degree of variation. Juvenile survival rates varied from 0.52 +/- 0.05 to 0.78 +/- 0.10 among sites and from 0.15 +/- 0.14 to 0.89 +/- 0.06 over time. Adult survival rates varied from 0.62 +/- 0.09 to 0.80 +/- 0.03 among sites, but did not vary significantly over time. We used reverse-time CMR models to estimate the realized population growth rate (lamda), and to investigate the influence of the observed variation in age-specific survival rates on lamda. The realized growth rate of the population closely covaried with, and was significantly influenced by, spatiotemporal variation in juvenile survival rate. High variability in juvenile survival rates over space and time clearly influenced the dynamics of our study population and is also likely to be an important determinant of the spatiotemporal variation in the population dynamics of other mammals with similar life history characteristics.     

A Bayesian approach to retransformation bias in transformed regression

Ecological data analysis often involves fitting linear or nonlinear equations to data after transforming either the response variable, the right side of the equation, or both, so that the standard suite of regression assumptions are more closely met. However, inference is usually done in the natural metric and it is well known that retransforming back to the original metric provides a biased estimator for the mean of the response variable. For the normal linear model, fit under a log-transformation, correction factors are available to reduce this bias, but these factors may not be generally applicable to all model forms or other transformations. We demonstrate that this problem is handled in a straightforward manner using a Bayesian approach, which is general for linear and nonlinear models and other transformations and model error structures. The Bayesian framework provides a predictive distribution for the response variable so that inference can be made at the mean, or over the entire distribution to incorporate the predictive uncertainty.     

Mercury in fish from two Nicaraguan lakes: a recommendation for increased monitoring of fish for international commerce

We measured total mercury concentrations in water and fish of Lake Managua and Lake Apoyo. Water mercury concentrations were 10-fold higher in Lake Managua than in Lake Apoyo, although differences in mercury concentration in the most common native fish were not significant. One-fourth of the commercially fished tilapia in Lake Managua exceeded maximum recommended mercury levels for consumption among pregnant women and other at-risk groups, although bioavailability to fishes was lower than in previously studied sites in Brazil and Western Maryland. The lower bioavailiability may present important information for management options to reduce mercury exposure to fishes and humans. We recommend closer mercury monitoring among freshwater fish destined for international commerce.     

Air-substrate mercury exchange associated with landfill disposal of coal combustion products

Previous laboratory studies have shown that lignite-derived fly ash emitted mercury (Hg) to the atmosphere, whereas bituminous- and subbituminous-derived fly ash samples adsorbed Hg from the air. In addition, wet flue gas desulfurization (FGD) materials were found to have higher Hg emission rates than fly ash. This study investigated in situ Hg emissions at a blended bituminous-subbituminous ash landfill in the Great Lakes area and a lignite-derived ash and FGD solids landfill in the Midwestern United States using a dynamic field chamber. Fly ash and saturated FGD materials emitted Hg to atmosphere at low rates (-0.1 to 1.2 ng/ m2hr), whereas FGD material mixed with fly ash and pyrite exhibited higher emission rates (approximately 10 ng/m2hr) but were still comparable with natural background soils (-0.3 to 13 ng/ m2hr). Air temperature, solar radiation, and relative humidity were important factors correlated with measured Hg fluxes. Field study results were not consistent with corresponding laboratory observations in that fluxes measured in the latter were higher and more variable. This is hypothesized to be partially an artifact of the flux measurement methods.     

Postnatal management of prenatally diagnosed abdominal masses and anomalies

Rapid advancement in fetal diagnostic imaging has increased our ability to diagnose a multitude of anomalies in the prenatal period. The purpose of this chapter is to review our current understanding of prenatally diagnosed intra-abdominal lesions, and describe the current guidelines for the postnatal management and subsequent outcome for these lesions. Copyright © 2008 John Wiley & Sons, Ltd.