Estimating abundance: a non parametric mark recapture approach for open and closed systems

We present a novel, non-parametric, frequentist approach for capture-recapture data based on a ratio estimator, which offers several advantages. First, as a non-parametric model, it does not require a known underlying distribution for parameters nor the associated assumptions, eliminating the need for post-hoc corrections or additional modeling to account for heterogeneity and other violated assumptions. Second, the model explicitly deals with dependence of trials by considering trials to be dependent; therefore, cluster sampling is handled naturally and additional adjustments are not necessary. Third, it accounts for ordering, utilizing the fact that a system with a small population will have a greater frequency of recaptures “early” in the survey work compared to an identical system with a larger population. We provide mathematical proof that our estimator attains asymptotic minimum variance under open systems. We apply the model to a data set of bottlenose dolphins (Tursiops truncatus) and compare results to those from classic closed models. We show that the model has an impressive rate of convergence and demonstrate that there’s an inverse relationship between population size and the proportion of the population that need to be sampled, while achieving the same degree of accuracy for abundance estimates. The model is flexible and can apply to ecological situations as well as other situations that lend themselves to capture recapture sampling.     

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.     

Spatial and social connectivity of fish-eating “Resident” killer whales (Orcinus orca) in the northern North Pacific

The productive North Pacific waters of the Gulf of Alaska, Aleutian Islands and Bering Sea support a high density of fish-eating “Resident” type killer whales (Orcinus orca), which overlap in distribution with commercial fisheries, producing both direct and indirect interactions. To provide a spatial context for these interactions, we analyzed a 10-year dataset of 3,058 whale photo-identifications from 331 encounters within a large (linear ~4,000 km) coastal study area to investigate the ranging and social patterns of 532 individually identifiable whales photographed in more than one encounter. Although capable of large-scale movements (maximum 1,443 km), we documented ranges generally <200 km, with high site fidelity across summer sampling intervals and also re-sightings during a winter survey. Bayesian analysis of pair-wise associations identified four defined clusters, likely representing groupings of stable matrilines, with distinct ranging patterns, that combined to form a large network of associated whales that ranged across most of the study area. This provides evidence of structure within the Alaska stock of Resident killer whales, important for evaluating ecosystem and fisheries impacts. This network included whales known to depredate groundfish from longline fisheries, and we suggest that such large-scale connectivity has facilitated the spread of depredation.     

Within-population variation in ejaculate characteristics in a prolonged breeder,Peron’s tree frog, <Emphasis Type="Italic">Litoria peronii</Emphasis>

Sperm number is often a good predictor of success in sperm competition; however, it has become increasingly clear that, for some species, variation in probability of paternity cannot be explained by sperm number alone. Intraspecific variation in ejaculate characteristics, such as the number of viable sperm and sperm longevity, may play an equally important role in determining fertilization success. Here, we assess variation among ejaculates in three factors that may contribute to fertilization success (number of sperm per ejaculate, viability, and longevity), in a population of Peron’s tree frog (Litoria peronii). We detected large variation among males in the number of sperm per ejaculate and the proportion of viable sperm within ejaculates, which could not be explained by variation in either male size or body condition. However, the proportion of viable sperm released by males increased over the season. Finally, we assessed sperm longevity (proportion viable sperm determined using a dual-fluorochrome vital dye) at two different temperatures. At 23°C, on average, 75% of sperm remained viable after 2 h, but there were significant differences amongst males with the percentage of viable sperm ranging from 43% to 95%. For sperm incubated at 4°C, ejaculates varied fivefold in sperm longevity with some males having 50% viable sperm after 5 days. Our data suggest that ejaculate characteristics (sperm number, viability, and longevity) vary widely in Peron’s tree frog and may therefore play an important role in determining siring success both in the presence and absence of sperm competition. We discuss the results in relation to selection on ejaculate traits via natural and sexual selection in this and other amphibians.     

Applying 3DCE to environmentally responsible manufacturing practices

A review of recent literature in the fields of operations, supply chain, and management indicates there is on-going interest in improving new product development (NPD) performance. Three-dimensional concurrent engineering (3DCE), the simultaneous design of product, process and supply chain have been proposed as a way to improve traditional NPD outcomes, such as reduced time to market, lower costs, and improved customer acceptance. There appears to be a lesser concern associated with the environmental impacts of new products. Environmentally responsible manufacturing (ERM) on new product development focuses on reduced emissions, hazardous materials elimination, and lower product weight without sacrificing functionality. This paper explores the following issue: will employing 3DCE to integrate NPD and ERM yield better benefits than the separate and uncoordinated application of environmental goals and NPD initiatives?     

Adaptive management for a turbulent future

The challenges that face humanity today differ from the past because as the scale of human influence has increased, our biggest challenges have become global in nature, and formerly local problems that could be addressed by shifting populations or switching resources, now aggregate (i.e., "scale up") limiting potential management options. Adaptive management is an approach to natural resource management that emphasizes learning through management based on the philosophy that knowledge is incomplete and much of what we think we know is actually wrong. Adaptive management has explicit structure, including careful elucidation of goals, identification of alternative management objectives and hypotheses of causation, and procedures for the collection of data followed by evaluation and reiteration. It is evident that adaptive management has matured, but it has also reached a crossroads. Practitioners and scientists have developed adaptive management and structured decision making techniques, and mathematicians have developed methods to reduce the uncertainties encountered in resource management, yet there continues to be misapplication of the method and misunderstanding of its purpose. Ironically, the confusion over the term "adaptive management" may stem from the flexibility inherent in the approach, which has resulted in multiple interpretations of "adaptive management" that fall along a continuum of complexity and a priori design. Adaptive management is not a panacea for the navigation of 'wicked problems' as it does not produce easy answers, and is only appropriate in a subset of natural resource management problems where both uncertainty and controllability are high. Nonetheless, the conceptual underpinnings of adaptive management are simple; there will always be inherent uncertainty and unpredictability in the dynamics and behavior of complex social-ecological systems, but management decisions must still be made, and whenever possible, we should incorporate learning into management.     

Source and Delivery of Nutrients to Receiving Waters in the Northeastern and Mid‐Atlantic Regions of the United States1

Moore, Richard B., Craig M. Johnston, Richard A. Smith, and Bryan Milstead, 2011. Source and Delivery of Nutrients to Receiving Waters in the Northeastern and Mid‐Atlantic Regions of the United States. Journal of the American Water Resources Association (JAWRA) 47(5):965‐990. DOI: 10.1111/j.1752‐1688.2011.00582.x Abstract: This study investigates nutrient sources and transport to receiving waters, in order to provide spatially detailed information to aid water‐resources managers concerned with eutrophication and nutrient management strategies. SPAtially Referenced Regressions On Watershed attributes (SPARROW) nutrient models were developed for the Northeastern and Mid‐Atlantic (NE US) regions of the United States to represent source conditions for the year 2002. The model developed to examine the source and delivery of nitrogen to the estuaries of nine large rivers along the NE US Seaboard indicated that agricultural sources contribute the largest percentage (37%) of the total nitrogen load delivered to the estuaries. Point sources account for 28% while atmospheric deposition accounts for 20%. A second SPARROW model was used to examine the sources and delivery of phosphorus to lakes and reservoirs throughout the NE US. The greatest attenuation of phosphorus occurred in lakes that were large relative to the size of their watershed. Model results show that, within the NE US, aquatic decay of nutrients is quite limited on an annual basis and that we especially cannot rely on natural attenuation to remove nutrients within the larger rivers nor within lakes with large watersheds relative to the size of the lake.     

Potential world garbage and waste carbon sequestration

To offset the carbon dioxide released by fossil fuels, a proposed sequestration strategy relies on burying garbage and waste in landfills. This paper roughly estimates the current annual world supply of carbonaceous waste to be 35.5 billion metric tons and to contain about 18 billion metric tons of carbon. If landfills received all of this waste, sequestration of more than 5.6 billion metric tons of carbon seems theoretically possible—an amount well in excess of the 3.3 billion metric tons which the atmosphere is currently gaining.