Calculating Ne and Ne/N in age-structured populations: a hybrid Felsenstein-Hill approach

The concept of effective population size (Ne) was developed under a discrete-generation model, but most species have overlapping generations. In the early 1970s, J. Felsenstein and W. G. Hill independently developed methods for calculating Ne in age-structured populations; the two approaches produce the same answer under certain conditions and have contrasting advantages and disadvantages. Here, we describe a hybrid approach that combines useful features of both. Like Felsenstein's model, the new method is based on age-specific survival and fertility rates and therefore can be directly applied to any species for which life table data are available. Like Hill, we relax the restrictive assumption in Felsenstein's model regarding random variance in reproductive success, which allows more general application. The basic principle underlying the new method is that age structure stratifies a population into winners and losers in the game of life: individuals that live longer have more opportunities to reproduce and therefore have a higher mean lifetime reproductive success. This creates different classes of individuals within the population, and grouping individuals by age at death provides a simple means of calculating lifetime variance in reproductive success of a newborn cohort. The new method has the following features: (1) it can accommodate unequal sex ratio and sex-specific vital rates and overdispersed variance in reproductive success; (2) it can calculate effective size in species that change sex during their lifetime; (3) it can calculate Ne and the ratio Ne/N based on various ways of defining N; (4) it allows one to explore the relationship between Ne and the effective number of breeders per year (Nb), which is a quantity that genetic estimators of contemporary Ne commonly provide information about; and (5) it is implemented in freely available software (AgeNe).     

Multivariate identification of plant functional response and effect traits in an agricultural landscape

Plant functional traits have been proposed as a linkage between the environmental control of vegetation and ecosystem function. Identification of traits that mediate the response of plant species to the environment is well established, but the identification of effect traits and the linkage between the two sets is less developed. This was attempted for a study of eight contrasting land uses in a marginal agricultural landscape where data on vegetation, management controls of the disturbance regime, and soil characteristics, including nitrogen release, were measured simultaneously with measures of ecosystem function such as litter decomposition rates and primary productivity on 30 sites. Trait data were assembled from databases, and an iterative multivariate approach using the three table (species, trait, environment) method RLQ was employed to identify a parsimonious set of traits that predict plant species responses to the environment and a parsimonious set of traits that link vegetation to ecosystem function. The lists of response and effect traits were similar, and where differences were observed, traits were usually highly correlated with at least one trait in the other list. This approach identified a small number of traits (canopy height, leaf dry matter content, leaf size, and specific leaf area) that provide a means of linking vegetation responses to environmental change with changes in ecosystem function. Other response traits included vegetative spread strategy, start of flowering, and seed terminal velocity, but within the system studied these traits were all significantly correlated to the traits shared between the response and effect lists.     

Directional changes in the species composition of a tropical forest

Long-term studies have revealed that the structure and dynamics of many tropical forests are changing, but the causes and consequences of these changes remain debated. To learn more about the forces driving changes within tropical forests, we investigated shifts in tree species composition over the past 25 years within the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI), Panama, and examined how observed patterns relate to predictions of (1) random population fluctuations, (2) carbon fertilization, (3) succession from past disturbance, (4) recovery from an extreme El Ni?o drought at the start of the study period, and (5) long-term climate change. We found that there have been consistent and directional changes in the tree species composition. These shifts have led to increased relative representations of drought-tolerant species as determined by the species' occurrence both across a gradient of soil moisture within BCI and across a wider precipitation gradient from a dry forest near the Pacific coast of Panama to a wet forest near its Caribbean coast. These nonrandom changes cannot be explained by stochastic fluctuations or carbon fertilization. They may be the legacy of the El Ni?o drought, or alternatively, potentially reflect increased aridity due to long-term climate change. By investigating compositional changes, we increased not only our understanding of the ecology of tropical forests and their responses to large-scale disturbances, but also our ability to predict how future global change will impact some of the critical services provided by these important ecosystems.     

Social parasitism of queens and workers in the Cape honeybee (<Emphasis Type="Italic">Apis mellifera capensis</Emphasis>)

Workers of a queenless honeybee colony can requeen the colony by raising a new queen from a young worker brood laid by the old queen. If this process fails, the colony becomes hopelessly queenless and workers activate their ovaries to lay eggs themselves. Laying Cape honeybee workers (Apis mellifera capensis) produce female offspring as an additional pathway for requeening. We tested the frequency of successful requeening in ten hopelessly queenless colonies. DNA genotyping revealed that only 8% of all queens reared in hopelessly queenless colonies were the offspring of native laying worker offspring. The vast majority of queens resulted from parasitic takeovers by foreign queens (27%) and invading parasitic workers (19%). This shows that hopelessly queenless colonies typically die due to parasitic takeovers and that the parasitic laying workers are an important life history strategy more frequently used than in providing a native queen to rescue the colony. Parasitism by foreign queens, which might enter colonies alone or accompanied by only a small worker force is much more frequent than previously considered and constitutes an additional life history strategy in Cape honeybees.     

Fish Migration, Dams, and Loss of Ecosystem Services in the Mekong Basin

The past decade has seen increased international recognition of the importance of the services provided by natural ecosystems. It is unclear however whether such international awareness will lead to improved environmental management in many regions. We explore this issue by examining the specific case of fish migration and dams on the Mekong river. We determine that dams on the Mekong mainstem and major tributaries will have a major impact on the basin’s fisheries and the people who depend upon them for food and income. We find no evidence that current moves towards dam construction will stop, and consider two scenarios for the future of the fisheries and other ecosystems of the basin. We conclude that major investment is required in innovative technology to reduce the loss of ecosystem services, and alternative livelihood strategies to cope with the losses that do occur.     

Effects of Heating Season on Residential Indoor and Outdoor Polycyclic Aromatic Hydrocarbons, Black Carbon, and Particulate Matter in an Urban Birth Cohort

Exposure to air pollutants has been associated with adverse health effects. However, analyses of the effects of season and ambient parameters such as ozone have not been fully conducted. Residential indoor and outdoor air levels of polycyclic aromatic hydrocarbons (PAH), black carbon (measured as absorption coefficient [Abs]), and fine particulate matter <2.5 μm (PM)(2.5) were measured over two-weeks in a cohort of 5-6 year old children (n=334) living in New York City's Northern Manhattan and the Bronx between October 2005 and April 2010. The objectives were to: 1) characterize seasonal changes in indoor and outdoor levels and indoor/outdoor (I/O) ratios of PAH (gas + particulate phase; dichotomized into Σ(8)PAH(semivolatile) (MW 178-206), and Σ(8)PAH(nonvolatile) (MW 228-278)), Abs, and PM(2.5); and 2) assess the relationship between PAH and ozone. Results showed that heating compared to nonheating season was associated with greater Σ(8)PAH(nonvolatile) (p<0.001) and Abs (p<0.05), and lower levels of Σ(8)PAH(semivolatile) (p<0.001). In addition, the heating season was associated with lower I/O ratios of Σ(8)PAH(nonvolatile) and higher I/O ratios of Σ(8)PAH(semivolatile) (p<0.001) compared to the nonheating season. In outdoor air, Σ(8)PAH(nonvolatile) was correlated negatively with community-wide ozone concentration (p<0.001). Seasonal changes in emission sources, air exchanges, meteorological conditions and photochemical/chemical degradation reactions are discussed in relationship to the observed seasonal trends.     

Natural resource dependence and the accumulation of physical and human capital in Latin America

In a simultaneous model of human and physical capital accumulation for 17 Latin American countries from 1975 to 2004, we show that overall resource dependence has no significant direct effect on physical and human capital. When disaggregating the natural resource variable into sub-categories, we find that petroleum export dependence has a significant positive direct effect on physical capital, but a significant negative direct effect on human capital. Agricultural export dependence shows a significant negative direct effect on physical capital. Petroleum exports have a long run positive effect on physical capital but a negative long run effect on human capital. Agricultural exports have a negative long run effect on physical and human capital.     

Trends in atmospheric reactive nitrogen for the Eastern United States

Reactive nitrogen can travel far from emission sources and impact sensitive ecosystems. From 2002 to 2006, policy actions have led to decreases in NO(x) emissions from power plants and motor vehicles. In this study, atmospheric chemical transport modeling demonstrates that these emissions reductions have led to a downward trend in ambient measurements of transported reactive nitrogen, especially atmospheric concentrations and wet deposition of nitrate. The trend in reduced nitrogen, namely ammonium, is ambiguous. As reduced nitrogen becomes a larger fraction of the reactive nitrogen budget, wide-spread NH(3) measurements and improved NH(3) emissions assessments are a critical need.     

HPLC determination of chlorate metabolism in bovine ruminal fluid

Salmonella and Escherichia coli are two bacteria that are important causes of human and animal disease worldwide. Chlorate is converted in the cell to chlorite, which is lethal to these bacteria. An HPLC procedure was developed for the rapid analysis of chlorate (ClO₃ ^?), nitrate (NO₃ ^?), and nitrite (NO₂ ^?) ions in bovine ruminal fluid samples. Standard curves for chlorite, nitrite, nitrate, and chlorate were well defined linear curves with R² values of 0.99846, 0.99106, 0.99854, and 0.99138, respectively. Concentrations of chlorite could not be accurately determined in bovine ruminal fluid because chlorite reacts with or binds a component(s) or is reduced to chloride in bovine ruminal fluid resulting in low chlorite measurements. A standard curve ranging from 25 to 150 ppm ClO₃ ^? ion was used to measure chlorate fortified into ruminal fluid. The concentration of chlorate was more rapidly lowered (P < 0.01) under anaerobic compared to aerobic incubation conditions. Chlorate alone or chlorate supplemented with the reductants sodium lactate or glycerol were bactericidal in anaerobic incubations. In anaerobic culture, the addition of sodium formate to chlorate-fortified ruminal fluid appeared to decrease chlorate concentrations; however, formate also appeared to moderate the bactericidal effect of chlorate against E. coli. Addition of the reductants, glycerol or lactate, to chlorate-fortified ruminal fluid did not increase the killing of E. coli at 24 h, but may be useful when the reducing equivalents are limiting as in waste holding reservoirs or composting systems required for intense animal production.     

Testing the Potential for Predictive Modeling and Mapping and Extending Its Use as a Tool for Evaluating Management Scenarios and Economic Valuation in the Baltic Sea (PREHAB)

We evaluated performance of species distribution models for predictive mapping, and how models can be used to integrate human pressures into ecological and economic assessments. A selection of 77 biological variables (species, groups of species, and measures of biodiversity) across the Baltic Sea were modeled. Differences among methods, areas, predictor, and response variables were evaluated. Several methods successfully predicted abundance and occurrence of vegetation, invertebrates, fish, and functional aspects of biodiversity. Depth and substrate were among the most important predictors. Models incorporating water clarity were used to predict increasing cover of the brown alga bladderwrack Fucus vesiculosus and increasing reproduction area of perch Perca fluviatilis, but decreasing reproduction areas for pikeperch Sander lucioperca following successful implementation of the Baltic Sea Action Plan. Despite variability in estimated non-market benefits among countries, such changes were highly valued by citizens in the three Baltic countries investigated. We conclude that predictive models are powerful and useful tools for science-based management of the Baltic Sea.