Much ado about nothings: using zero similarity points in distance-decay curves

Distance decay is used to describe the (usually exponential) decay in ecological similarity of assemblages between two sites as a function of their distance apart along an environmental gradient. Exponential distance-decay curves are routinely fitted by calculating the ecological similarity between each pair of sites, and fitting a linear regression to the points on a scatter plot of log-similarity vs. distance (x-axis). However, pairs of sites where the assemblages have no species in common pose a problem, because the similarity is zero, and the log transformation cannot be applied. Common fixes to this problem (i.e., either removing or transforming the zero values) are shown to have undesirable consequences and to give widely disparate estimates. A new method is presented as a special case of a generalized dissimilarity model. It is fitted very quickly and easily using existing software, and it does not require removal or transformation of the zero similarity points. Its simplicity makes it convenient for use in conjunction with the resampling methods that are routinely employed to test hypotheses, to obtain standard errors of estimated parameters, or to compare distance-decay curves. A word of caution about standard application of the bootstrap is noted, and modified bootstrap and jackknife alternatives are demonstrated.     

Habitat biodiversity as a determinant of fish community structure on coral reefs

Increased habitat diversity is often predicted to promote the diversity of animal communities because a greater variety of habitats increases the opportunities for species to specialize on different resources and coexist. Although positive correlations between the diversities of habitat and associated animals are often observed, the underlying mechanisms are only now starting to emerge, and none have been tested specifically in the marine environment. Scleractinian corals constitute the primary habitat-forming organisms on coral reefs and, as such, play an important role in structuring associated reef fish communities. Using the same field experimental design in two geographic localities differing in regional fish species composition, we tested the effects of coral species richness and composition on the diversity, abundance, and structure of the local fish community. Richness of coral species overall had a positive effect on fish species richness but had no effect on total fish abundance or evenness. At both localities, certain individual coral species supported similar levels of fish diversity and abundance as the high coral richness treatments, suggesting that particular coral species are disproportionately important in promoting high local fish diversity. Furthermore, in both localities, different microhabitats (coral species) supported very different fish communities, indicating that most reef fish species distinguish habitat at the level of coral species. Fish communities colonizing treatments of higher coral species richness represented a combination of those inhabiting the constituent coral species. These findings suggest that mechanisms underlying habitat-animal interaction in the terrestrial environment also apply to marine systems and highlight the importance of coral diversity to local fish diversity. The loss of particular key coral species is likely to have a disproportionate impact on the biodiversity of associated fish communities.     

Classification of multiple types of organic carbon composition in atmospheric particles by scanning transmission X-ray microscopy analysis

A scanning transmission X-ray microscope at the Lawrence Berkeley National Laboratory is used to measure organic functional group abundance and morphology of atmospheric aerosols. We present a summary of spectra, sizes, and shapes observed in 595 particles that were collected and analyzed between 2000 and 2006. These particles ranged between 0.1 and 12 μm and represent aerosols found in a large range of geographical areas, altitudes, and times. They include samples from seven different field campaigns: PELTI, ACE-ASIA, DYCOMS II, Princeton, MILAGRO (urban), MILAGRO (C-130), and INTEX-B. At least 14 different classes of organic particles show different types of spectroscopic signatures. Different particle types are found within the same region while the same particle types are also found in different geographical domains. Particles chemically resembling black carbon, humic-like aerosols, pine ultisol, and secondary or processed aerosol have been identified from functional group abundance and comparison of spectra with those published in the literature.     

Organic and Inorganic Characterization of Marine Colloids

Isolates of the organic matter in the particulate, colloidal and dissolved states were obtained by tangential flow ultrafiltration through 0.40 μm polycarbonate and ∼ 1 nm (1000 NMWL*) regenerated cellulose membranes and by solid-liquid reverse phase extraction techniques. the material was analyzed qualitatively by mass spectroscopy, proton nuclear magnetic resonance, Fourier transform infrared spectroscopy, high performance liquid chromatography with fluorescence detection of labelled primary amines and amino acids, and inductively coupled plasma/mass spectroscopy. All three states are characterized by similar organic chemistries. the marine colloidal state in coastal waters off the Californian coast contains primarily carbohydrates, fatty acids, minor amounts of proteinaceous compounds and electropositive elements including aluminium and iron. Aromatic molecules and olefinic functional groups are in low concentration. the colloidal state differs qualitatively from the particulate and dissolved states. Yet all three could be derived, with degradation, from algal or macroalgal surface components.     

Growth and mortality of subtidal red sea urchins (Strongylocentrotus franciscanus) at San Nicolas Island,California, USA: problems with models

Red sea urchins, Strongylocentrotus franciscanus, were tagged with tetracycline in 1990 at subtidal sites off San Nicolas Island, California, USA. After one year in the field, the sea urchins were collected and growth increments were measured based on tetracycline marks, which indicated initial slow growth, a maximum rate, and finally a prolonged period of very slow growth. Small red sea urchins (4 cm diam) were estimated to be 3 to 4 yr old, which is much older than has previously been reported. It is estimated that about 12 yr would be required to attain 10 cm diam. Survival has previously been modeled assuming a constant rate. If the population of red sea urchins is assumed to be stable and stationary, annual survival rate was between 71 and 77% yr^-1. Census data for the two years of study have permitted annual survival to be estimated without assuming stable and stationary population structure. Under these conditions, annual survival rate was between 79 and 86% yr^-1. Analysis of transitions in the size distributions from 1990 to 1991 suggested that annual survival may have been sizespecific: 91% yr^-1 for individuals 1.1 to 4.0 cm diam, 82% yr^-1 for individuals 4.1 to 7.0 cm diam, and 63% yr^-1 for those of 7.1 to 10.0 cm diam. An alternative explanation to size-specific survival in our study is sizespecific immigration.     

Thermodynamics of NaHCO3 decomposition during Na2CO3-based CO2 capture

Amine-basedcarbon-capture technologies have been shown to be energetically expensive and to cause significant environmental and epidemiological impacts due to their volatility.Bicarbonate formation from carbon dioxide's reaction with water has been suggested as an effective alternative for capturing CO_2;however,the thermodynamics of this reaction are not well understood.This study experimentally determined the equilibrium constant of sodium bicarbonate(Na HCO_3)decomposition to sodium,water,and carbon dioxide;the study also compared the equilibrium constant to theoretical calculations.Using a combination of experimentation and thermodynamic relationships,the unitless equilibrium constants of the forward and reverse reactions were calculated accurately(error±9%and±4%,respectively).Equilibrium data were calculated using enthalpy and entropy values of each component of Na HCO_3decomposition at temperatures ranging from 25 to 155°C respectively.These results offer more data essential to optimizing Na HCO_3use in environmentally friendly nextgeneration CO_2-capture technologies.     

Food availability at birth limited reproductive success in historical humans

Environmental conditions in early life can profoundly affect individual development and have consequences for reproductive success. Limited food availability may be one of the reasons for this, but direct evidence linking variation in early-life nutrition to reproductive performance in adulthood in natural populations is sparse. We combined historical agricultural data with detailed demographic church records to investigate the effect of food availability around the time of birth on the reproductive success of 927 men and women born in 18th-century Finland. Our study population exhibits natural mortality and fertility rates typical of many preindustrial societies, and individuals experienced differing access to resources due to social stratification. We found that among both men and women born into landless families (i.e., with low access to resources), marital prospects, probability of reproduction, and offspring viability were all positively related to local crop yield during the birth year. Such effects were generally absent among those born into landowning families. Among landless individuals born when yields of the two main crops, rye and barley, were both below median, only 50% of adult males and 55% of adult females gained any reproductive success in their lifetime, whereas 97% and 95% of those born when both yields were above the median did so. Our results suggest that maternal investment in offspring in prenatal or early postnatal life may have profound implications for the evolutionary fitness of human offspring, particularly among those for which resources are more limiting. Our study adds support to the idea that early nutrition can limit reproductive success in natural animal populations, and provides the most direct evidence to date that this process applies to humans.     

Cobalt speciation assay for human serum,Part I. Method for measuring large and small molecular cobalt and protein-binding capacity using size exclusion chromatography with inductively coupled plasma-mass spectroscopy detection

A method utilizing size exclusion liquid chromatography (SEC) was developed to separate and quantify large molecular cobalt (Co) (e.g., albumin-Co) from cyanocobalamin (vitamin B₁₂) and small molecular Co (e.g., glutathione-Co and free Co) in human serum. Highly selective and sensitive detection using inductively coupled plasma–mass spectrometry was coupled with SEC to provide a method with reliable accuracy, precision, recoveries, stability, and a detection limit of 0.037 μg/L in undiluted serum. Other divalent metal cations known to compete with Co(II) for serum albumin-binding sites (such as iron, zinc, manganese, cadmium, copper, nickel, and lead) did not significantly alter Co(II) quantification. Co–protein binding capacity determination of individual serum samples indicated that addition of 2500 μg Co/L to undiluted human serum resulted in approximately 90% distribution to the large molecular Co peak, consistent with Co binding to high-affinity divalent metal binding sites on albumin. Since serum albumin binding partially sequesters biologically active Co(II) ions, this method provides an important tool for better understanding the kinetics and toxicology of Co compounds. Thus, the proposed method might play an important role in establishing Co dose–response relationships that affect the equilibrium concentrations of free ionic Co(II).     

Costs of expanding the network of protected areas as a response to climate change in the Cape Floristic Region

The expansion of protected areas is a critical component of strategies to promote the continued existence of biodiversity (i.e., life at all levels of biological organization) as climate changes, but scientific, social, and economic uncertainties associated with climate change are some of the major obstacles preventing such expansion. New models of climate change and species distribution and new methods of conservation planning now make it possible to explore the uncertainties associated with climate changes and species responses. Yet few reliable estimates of the costs of expanding protected areas and methods for determining these costs exist, largely because of the many (and uncertain) determinants of these costs. We developed a cost-accounting model to estimate the range in costs of various options for expanding protected areas and to explore the variables that drive these costs. Model development was informed by an existing plan to expand protected areas in the Cape Floristic Region of South Africa to address species conservation under a scenario of climate change. The 50-year present value of total costs varied from US$260 million ($1077/ha) for an off-reserve option that involves agreements with landowners and no compensation of forgone production and associated revenue to $1020 million ($4228/ha) for an on-reserve option that involves land acquisition and protection. The costs of acquiring land or compensating landowners for forgone production and development opportunities were the major drivers of the total costs across all options because most of the area identified in the protected-area expansion plan consisted of urban and high-quality agricultural lands. Total costs were also affected by changes in protected area extent and discount rate. Model-generated outputs such as these may be useful for informing implementation strategies and the allocation of future efforts in monitoring, data collection, and model development.     

Defeated chameleons darken dynamically during dyadic disputes to decrease danger from dominants

Research on intraspecific aggression has typically focused on dominant individuals, but a better understanding of the consequences and mechanisms of agonistic encounters requires a balanced perspective that includes knowledge of subordinate animal behaviors. In contrast to signals of fighting ability, signals of submission are an understudied component of agonistic communication that could provide important insights into the dynamics, function, and evolution of intraspecific competition. Here, I use a series of staged agonistic trials between adult male veiled chameleons Chamaeleo calyptratus to test the hypothesis that rapid skin darkening serves as a submissive signal to resolve agonistic activity. Concordant with this hypothesis, I found that losing chameleons darkened over the course of aggressive trials while winners brightened, and the likelihood of darkening increased when individuals were attacked more aggressively. Additionally, I found that the degree of brightness change exhibited by individual chameleons was tied to both overall and net aggression experienced during a trial, with chameleons who received high levels of aggression relative to their own aggression levels darkening to a greater extent than individuals receiving relatively less aggression. Lastly, I found that aggression increased for losers and winners prior to the onset of darkening by the eventual loser but that both chameleons reduced aggression after the losing chameleon began to darken. Based on the theoretical prediction that signals of submission should be favored when retreat options are restricted, I suggest that limited escapability imposed by chameleon morphology, physiology, and ecology favored the evolution of a pigment-based signal of submission in this group.