Bayesian analysis of Jolly-Seber type models

We propose the use of finite mixtures of continuous distributions in modelling the process by which new individuals, that arrive in groups, become part of a wildlife population. We demonstrate this approach using a data set of migrating semipalmated sandpipers (Calidris pussila) for which we extend existing stopover models to allow for individuals to have different behaviour in terms of their stopover duration at the site. We demonstrate the use of reversible jump MCMC methods to derive posterior distributions for the model parameters and the models, simultaneously. The algorithm moves between models with different numbers of arrival groups as well as between models with different numbers of behavioural groups. The approach is shown to provide new ecological insights about the stopover behaviour of semipalmated sandpipers but is generally applicable to any population in which animals arrive in groups and potentially exhibit heterogeneity in terms of one or more other processes.     

Microbial communities biostimulated by ethanol during uranium (VI) bioremediation in contaminated sediment as shown by stable isotope probing

Stable isotope probing (SIP) was used to identify microbes stimulated by ethanol addition in microcosms containing two sediments collected from the bioremediation test zone at the US Department of Energy Oak Ridge site, TN, USA. One sample was highly bioreduced with ethanol while another was less reduced. Microcosms with the respective sediments were amended with ¹³C labeled ethanol and incubated for 7 days for SIP. Ethanol was rapidly converted to acetate within 24 h accompanied with the reduction of nitrate and sulfate. The accumulation of acetate persisted beyond the 7 d period. Aqueous U did not decline in the microcosm with the reduced sediment due to desorption of U but continuously declined in the less reduced sample. Microbial growth and concomitant ¹³C-DNA production was detected when ethanol was exhausted and abundant acetate had accumulated in both microcosms. This coincided with U(VI) reduction in the less reduced sample. ¹³C originating from ethanol was ultimately utilized for growth, either directly or indirectly, by the dominant microbial community members within 7 days of incubation. The microbial community was comprised predominantly of known denitrifiers, sulfate-reducing bacteria and iron (III) reducing bacteria including Desulfovibrio, Sphingomonas, Ferribacterium, Rhodanobacter, Geothrix, Thiobacillus and others, including the known U(VI)-reducing bacteria Acidovorax, Anaeromyxobacter, Desulfovibrio, Geobacter and Desulfosporosinus. The findings suggest that ethanol biostimulates the U(VI)-reducing microbial community by first serving as an electron donor for nitrate, sulfate, iron (III) and U(VI) reduction, and acetate which then functions as electron donor for U(VI) reduction and carbon source for microbial growth.     

Biological and environmental influences on the trophic ecology of leatherback turtles in the northwest Atlantic Ocean

Understanding the causes and consequences of variability in trophic status is important for interpreting population dynamics and for identifying important habitats for protected species like marine turtles. In the northwest Atlantic Ocean, many leatherback turtles (Dermochelys coriacea) from distinct breeding stocks throughout the Wider Caribbean region migrate to Canadian waters seasonally to feed, but their trophic status during the migratory and breeding cycle and its implications have not yet been described. In this study, we used stable carbon and nitrogen isotope analyses of bulk skin to characterize the trophic status of leatherbacks in Atlantic Canadian waters by identifying trophic patterns among turtles and the factors influencing those patterns. δ¹⁵N values of adult males and females were significantly higher than those of turtles of unknown gender (i.e., presumed to be subadults), and δ¹⁵N increased significantly with body size. We found no significant differences among average stable isotope values of turtles according to breeding stock origin. Significant inter-annual variation in δ¹⁵N among cohorts probably reflects broad-scale oceanographic variability that drives fluctuations in stable isotope values of nutrient sources transferred through several trophic positions to leatherbacks, variation in baseline isotope values among different overwintering habitats used by leatherbacks, or a combination of both. Our results demonstrate that understanding effects of demographic and physiological factors, as well as oceanographic conditions, on trophic status is key to explaining observed patterns in population dynamics and for identifying important habitats for widely distributed, long-lived species like leatherbacks.     

Habitat,movements and environmental preferences of dusky sharks,Carcharhinus obscurus,in the northern Gulf of Mexico

The dusky shark (Carcharhinus obscurus) is the largest member of the genus Carcharhinus and inhabits coastal and pelagic ecosystems circumglobally in temperate, subtropical and tropical marine waters. In the western North Atlantic Ocean (WNA), dusky sharks are overfished and considered vulnerable by the International Union for the Conservation of Nature. As a result, retention of dusky sharks in commercial and recreational fisheries off the east coast of the United States (US) and in the northern Gulf of Mexico is prohibited. Despite the concerns regarding the status of dusky sharks in the WNA, little is known about their habitat utilization. During the summers of 2008–2009, pop-up satellite archival tags were attached to ten dusky sharks (one male, nine females) at a location where they have been observed to aggregate in the north central Gulf of Mexico southwest of the Mississippi River Delta to examine their movement patterns and habitat utilization. All tags successfully transmitted data with deployment durations ranging from 6 to 124 days. Tag data revealed shark movements in excess of 200 km from initial tagging locations, with sharks primarily utilizing offshore waters associated with the continental shelf edge from Desoto Canyon to the Texas/Mexican border. While most sharks remained in US waters, one individual moved from the northern Gulf of Mexico into the Bay of Campeche off the coast of Mexico. Sharks spent 87 % of their time between 20 and 125 m and 83 % of their time in waters between 23 and 30 °C. Since dusky sharks are among the most vulnerable shark species to fishing mortality, there is a recovery plan in place for US waters; however, since they have been shown to make long-distance migrations, a multi-national management plan within the WNA may be needed to ensure the successful recovery of this population.     

Is male rhesus macaque red color ornamentation attractive to females?

Male sexually selected traits can evolve through different mechanisms: conspicuous and colorful ornaments usually evolve through intersexual selection, while weapons usually evolve through intra-sexual selection. Male ornaments are rare among mammals in comparison to birds, leading to the notion that female mate choice generally plays little role in trait evolution in this taxon. Supporting this view, when ornaments are present in mammals, they typically indicate social status and are products of male-male competition. This general mammalian pattern, however, may not apply to rhesus macaques (Macaca mulatta). Males of this species display conspicuous skin coloration, but this expression is not correlated to dominance rank and is therefore unlikely to have evolved due to male-male competition. Here, we investigate whether male color expression influences female proceptivity toward males in the Cayo Santiago free-ranging rhesus macaque population. We collected face images of 24 adult males varying in dominance rank and age at the peak of the mating season and modeled these to rhesus macaque visual perception. We also recorded female sociosexual behaviors toward these males. Results show that dark red males received more sexual solicitations, by more females, than pale pink ones. Together with previous results, our study suggests that male color ornaments are more likely to be a product of inter- rather than intra-sexual selection. This may especially be the case in rhesus macaques due to the particular characteristics of male-male competition in this species.     

Three-dimensional analysis of coherent turbulent flow structure around a single circular bridge pier

The coherent turbulent flow around a single circular bridge pier and its effects on the bed scouring pattern is investigated in this study. The coherent turbulent flow and associated shear stresses play a major role in sediment entrainment from the bed particularly around a bridge pier where complex vortex structures exist. The conventional two-dimensional quadrant analysis of the bursting process is unable to define sediment entrainment, particularly where fully three-dimensional flow structures exist. In this paper, three-dimensional octant analysis was used to improve understanding of the role of bursting events in the process of particle entrainment. In this study, the three-dimensional velocity of flow was measured at 102 points near the bed of an open channel using an Acoustic Doppler Velocity meter (Micro-ADV). The pattern of bed scouring was measured during the experiment. The velocity data were analysed using the Markov process to investigate the sequential occurrence of bursting events and to determine the transition probability of the bursting events. The results showed that external sweep and internal ejection events were an effective mechanism for sediment entrainment around a single circular bridge pier. The results are useful in understanding scour patterns around bridge piers.     

Riparian vegetation and channel morphology impact on spatial patterns of water quality in agricultural watersheds

A model based on theKLS factors of the Universal Soil Loss Equation (USLE) accurately predicted temporal dynamics and relative peak levels of suspended solids, turbidity, and phosphorus in an agricultural watershed with well-protected streambanks and cultivation to the stream edge. Fine suspended solids derived from surface runoff appeared to be a major component of the suspended solids in this stream. The model did not predict the same parameters in a watershed with unstable channel substrates, exposed streambanks, and heterogeneity in riparian vegetation and channel morphology. The rate of increase in concentration of the water quality parameters was higher than predicted in areas without riparian vegetation and with unstable substrates. Peak levels were higher than predicted where unstable channel substrates occurred, and potential energy of the stream was high because of stream alterations (removal of near-stream vegetation and creation of a uniform, straight channel). Timing of the peak levels of suspended solids, turbidity, and phosphorus in these areas seemed related to major flushes of discharge due to delayed inputs from the surface or subsurface or both or to rapid urban drainage. Higher suspended solids concentration in this stream seemed to involve larger quantities of large particles. Thus, the USLE may not adequately predict relative water quality conditions within a watershed when variation in channel morphology and riparian vegetation exists. We make the following recommendations:

1. Models to predict water quality effects of management programs should combine a terrestrial phase (which details hydrologic and erosion processes associated with surface runoff) with an aquatic phase (which details hydrologic processes of scour and sediment transport in channels). The impact of near-channel areas on these hydrologic processes should receive special attention.
2. Sampling schemes should be designed to account for the impact on water quality of both watershed land surface and inand near-channel processes. In order to help distinguish sources of suspended solids, researchers should emphasize analysis of size distribution of particles transported.
3. Best management systems for improving the broadest range of water resources in agricultural watersheds need to be based on an expanded “critical area” approach, which includes identification of critical erosive and depositional areas in both terrestrial and aquatic environments.

     

Mercury exposure through diet in pregnant women and women of childbearing age

The study examined the stage of clean-up of the Port Lavaca bay sites in Texas, which were polluted during the early 1990's by effluent containing mercury (Hg) from a chloralkali plant. In addition to Hg intoxication through environmental contaminations, human exposure through dietary fish and other seafoods occurred. Bacteria converts inorganic Hg to alkyl organic compounds and subsequently the metal crosses the blood brain barrier thus exerting adverse effects on the fetal developing nervous system. In order to conduct a survey of dietary Hg exposure, blood was collected from pregnant women and those of childbearing age at routine clinic visits at each of three centers in South Texas cities (Galveston, Texas City, Port Lavaca/Victoria, TX). A questionnaire sought dietary and lifestyle information including consumption, sources of fish and other seafoods. A significant number of subjects (119 out of 175, 68%) ate fish caught locally. The blood Hg concentrations (µg?L^?1) range varied with the location of the study centers: City of Galveston 2.6–62; Texas City 2.8–111.8; and the Port Lavaca areas 3.02–126.7. The concentrations of blood Hg was directly proportional to the number of fish meals consumed for each species considered. Mean blood Hg concentrations for no fish meals per week were: Port Lavaca 4.5 (N?=?3), Galveston 4.3 (N?=?3), Texas City 3.5 (N?=?10). For >3 fish meals per week, the mean blood Hg concentrations were: Port Lavaca, 48.0 (N?=?53), Galveston 29.1 (N?=?35), Texas City, 36.1 (N?=?31). Data show that residues of Hg were still present in 1994 despite the clean-up efforts.     

Polycyclic aromatic hydrocarbons in surface sediments held in experimental mesocosms

Sediment was collected from three locations along a pollution gradient in Narragansett Bay and transplanted to controlled mesocosms. Total hydrocarbons and eleven individual polycyclic aromatic hydrocarbons (PAHs) were measured in these sediments over a period of 394 days. Total hydrocarbon concentrations increased in the “relatively uncontaminated”; (Rhode Island Sound) sediment that was held in the mesocosms, but did not change in the two other sediments. The concentrations of four PAHs: naphthalene, 2‐methyl naphthalene, 1‐methyl naphthalene and biphenyl, decreased in the “contaminated”; (Providence River) sediment during the experiment and the calculated half‐lives for these compounds were 287, 353, 321 and 333 days, respectively.