Methods for joint inference from panel survey and demographic data

A number of methods for joint inference from animal abundance and demographic data have been proposed in recent years, each with its own advantages. A new approach to analyzing panel survey and demographic data simultaneously is described. The approach fits population-dynamics models to the survey data, rather than to a single index of abundance derived from them and thus avoids disadvantages inherent in analyzing such an index. The methodology is developed and illustrated with British Lapwing data, and the results are compared with those obtained from existing approaches. The estimates of demographic parameters and population indices are similar for all methods. The results of a simulation study show that the new method performs well in terms of mean squared error.     

Incorporating Climate and Ocean Change into Extinction Risk Assessments for 82 Coral Species

Many marine invertebrate species facing potential extinction have uncertain taxonomies and poorly known demographic and ecological traits. Uncertainties are compounded when potential extinction drivers are climate and ocean changes whose effects on even widespread and abundant species are only partially understood. The U.S. Endangered Species Act mandates conservation management decisions founded on the extinction risk to species based on the best available science at the time of consideration—requiring prompt action rather than awaiting better information. We developed an expert‐opinion threat‐based approach that entails a structured voting system to assess extinction risk from climate and ocean changes and other threats to 82 coral species for which population status and threat response information was limited. Such methods are urgently needed because constrained budgets and manpower will continue to hinder the availability of desired data for many potentially vulnerable marine species. Significant species‐specific information gaps and uncertainties precluded quantitative assessments of habitat loss or population declines and necessitated increased reliance on demographic characteristics and threat vulnerabilities at genus or family levels. Adapting some methods (e.g., a structured voting system) used during other assessments and developing some new approaches (e.g., integrated assessment of threats and demographic characteristics), we rated the importance of threats contributing to coral extinction risk and assessed those threats against population status and trend information to evaluate each species’ extinction risk over the 21st century. This qualitative assessment resulted in a ranking with an uncertainty range for each species according to their estimated likelihood of extinction. We offer guidance on approaches for future biological extinction risk assessments, especially in cases of data‐limited species likely to be affected by global‐scale threats. Incorporación del Cambio Climático y Oceánico en Estudios de Riesgo de Extinción para 82 Especies de Coral     

A note on data augmentation and iterative simulation for survival rate estimation

In this paper we examine the use of data augmentation techniques for simplifying iterative simulation in the context of both Bayesian and classical statistical inference for survival rate estimation. We examine two distinct model families common in population ecology to illustrate our ideas, ring-recovery models and capture–recapture models, and we present the computational advantage of this approach. We discuss also the fact that problems associated with identifiability in the classical framework can be overcome using data augmentation, but highlight the dangers in doing so under both inferential paradigms.

Using hidden Markov chains and empirical Bayes change-point estimation for transect data

Consider a lattice of locations in one dimension at which data are observed. We model the data as a random hierarchical process. The hidden process is assumed to have a (prior) distribution that is derived from a two-state Markov chain. The states correspond to the mean values (high and low) of the observed data. Conditional on the states, the observations are modelled, for example, as independent Gaussian random variables with identical variances. In this model, there are four free parameters: the Gaussian variance, the high and low mean values, and the transition probability in the Markov chain. A parametric empirical Bayes approach requires estimation of these four parameters from the marginal (unconditional) distribution of the data and we use the EM-algorithm to do this. From the posterior of the hidden process, we use simulated annealing to find the maximum a posteriori (MAP) estimate. Using a Gibbs sampler, we also obtain the maximum marginal posterior probability (MMPP) estimate of the hidden process. We use these methods to determine where change-points occur in spatial transects through grassland vegetation, a problem of considerable interest to plant ecologists.     

Testing sustainability by prospective and retrospective demographic analyses: evaluation for palm leaf harvest.

Harvesting nontimber forest products (NTFPs) is a major economic activity in tropical forests. As many NTFPs are overexploited, sustainability analyses are required to set harvest guidelines. Here we introduce and apply a new approach to evaluating sustainability, which combines prospective (elasticity) and retrospective (Life Table Response Experiments [LTRE]) demographic analyses of matrix population models. We relate the elasticity of vital rates (representing their importance for population growth rate, lamda) to their contribution to harvest-induced change in lamda ("LTRE contribution"). When high-elasticity vital rates have a low LTRE contribution, exploitation is potentially sustainable as negative effects for population growth are buffered. If the reverse is found, there is little scope for sustainability because crucial vital rates are affected. Our approach is less sensitive to chance fluctuations than the commonly used sustainability criterion of lamda = 1.0, as it does not depend on the absolute value of lamda. We applied this analysis to Geonoma deversa, a clustered forest understory palm. We studied three experimentally defoliated and control populations in a Bolivian rainforest during two years. Cutting all leaves of large ramets did not change mortality but strongly affected growth and reproduction. In spite of severe changes in some vital rates, population growth rate was not significantly reduced after defoliation. A literature review revealed that six other understory palms species responded very similarly to defoliation. The combination of LTRE contributions and elasticity analyses showed that low-elasticity vital rates were mainly responsible for the defoliation-induced change in lamda for Geonoma deversa. For two other understory palms (Astrocaryum mexicanum and Chamaedorea radicalis) new demographic analyses yielded very similar results. For Geonoma, the LTRE contribution-elasticity relation strongly changed when we mimicked harvest damage. Adding 5% mortality to defoliated palms caused stronger change in lamda, mainly due to changes in a high-elasticity vital rate (survival). Therefore, harvest practices that involve stem killing are clearly unsustainable. Our results show that commercial leaf cutting in Geonoma deversa is potentially sustainable, and that this is likely the case for understory palms in general. Our approach to evaluating harvest sustainability can be applied to other NTFPs.     

Energetics of early development for the sea urchinsStrongylocentrotus purpuratus andLytechinus pictus and the crustaceanArtemia sp.

Embryos and larvae of two species of sea urchin,Strongylocentrotus purpuratus andLytechinus pictus, and larvae of the brine shrimpArtemia sp. (San Francisco brand) were cultured to investigate the contribution of dissolved organic material in seawater to the energetics of early development. When embroys ofS. purpuratus were reared in artificial seawater, a net loss in dry organic mass was observed. In contrast, when sibling embryos were reared to Day 2 under identical conditions in natural seawater, there was either a net increase in dry organic mass or no change. A net decrease in mass was observed in only one of five cultures reared in filtered natural seawater. Energy budgets for each species were determined by giving energy equivalents to the changes in carbohydrate, lipid and protein, and to the rate of oxygen consumption for each day of development. In the case ofS. purpuratus, the use of endogenous reserves accounted for either 0 or 38% of the metabolic demand for two independent cultures reared from Days 0 to 2. For larvae ofL. pictus, reared to 8 d, only 66% of the metabolic demand could be accounted for by the use of endogenous reserves. Sea urchins are capable of transporting dissolved organic material from seawater. Calculations revealed that the energy deficit during the early development of sea urchins (S. purpuratus) could be accounted for by the uptake of dissolved organic matter from seawater. However, for a species that cannot use this resource (Artemia sp.), the metabolic needs during development are supplied through the use of endogenous reserves.     

Statistics for correlated data: phylogenies, space, and time.

Here we give an introduction to the growing number of statistical techniques for analyzing data that are not independent realizations of the same sampling process--in other words, correlated data. We focus on regression problems, in which the value of a given variable depends linearly on the value of another variable. To illustrate different types of processes leading to correlated data, we analyze four simulated examples representing diverse problems arising in ecological studies. The first example is a comparison among species to determine the relationship between home-range area and body size; because species are phylogenetically related, they do not represent independent samples. The second example addresses spatial variation in net primary production and how this might be affected by soil nitrogen; because nearby locations are likely to have similar net primary productivity for reasons other than soil nitrogen, spatial correlation is likely. In the third example, we consider a time-series model to ask whether the decrease in density of a butterfly species is the result of decreases in its host-plant density; because the population density of a species in one generation is likely to affect the density in the following generation, time-series data are often correlated. The fourth example combines both spatial and temporal correlation in an experiment in which prey densities are manipulated to determine the response of predators to their food supply. For each of these examples, we use a different statistical approach for analyzing models of correlated data. Our goal is to give an overview of conceptual issues surrounding correlated data, rather than a detailed tutorial in how to apply different statistical techniques. By dispelling some of the mystery behind correlated data, we hope to encourage ecologists to learn about statistics that could be useful in their own work. Although at first encounter these techniques might seem complicated, they have the power to simplify ecological research by making more types of data and experimental designs open to statistical evaluation.     

Niche differentiation and fine-scale projections for Argentine ants based on remotely sensed data.

Modeling ecological niches of species is a promising approach for predicting the geographic potential of invasive species in new environments. Argentine ants (Linepithema humile) rank among the most successful invasive species: native to South America, they have invaded broad areas worldwide. Despite their widespread success, little is known about what makes an area susceptible--or not--to invasion. Here, we use a genetic algorithm approach to ecological niche modeling based on high-resolution remote-sensing data to examine the roles of niche similarity and difference in predicting invasions by this species. Our comparisons support a picture of general conservatism of the species' ecological characteristics, in spite of distinct geographic and community contexts.     

Methods for chemical conversion of plastic wastes into fuels and chemicals. A review

Plastics are utilized in various materials that are useful in everyday life. As the usage of plastics increases, the disposal of plastic materials has become a major issue, calling for recycling methods. Here, we review the different methods to recycle plastics, with focus on catalytic cracking. We present catalysts, cracking mechanisms, and we compare the various treatment methodologies. Several attempts were made by researchers to increase the efficiency of the cracking process using different catalysts and reactors. Many studies reveal high quality products are obtained by catalytic cracking, which consumes low energy and produces lesser residues when compared to other treatment technologies.

     

Principal components derived from soil physicochemical data explained a land degradation gradient,and suggested the applicability of new indexes for estimation of soil productivity in the Sakaerat Environmental Research Station,Thailand

To find a principal component (PC) that quantifies the degree of soil degradation, we analyzed various physicochemical characteristics of soils over a land degradation gradient related to aboveground vegetation in the Sakacrat Environmental Research Station (SERS), Thailand. The aboveground vegetative types representing the degradation gradient were bare ground (BG, highly degraded), dry dipterocarp forest (DDF, moderately disturbed) and dry evergreen forest (DEF, the original vegetation). Soils under these vegetative types were sampled in February (dry season). March just after temporal precipitation) and June (rainy season) 2001. Through the period of this research, the degradation was consistently explained by sandy texture, high bulk density, lower pH, high exchangeable acidity, poor mineral and organic nutrients and dryness. Principal component analysis (PCA) was applied to determine significant principal components (PCs) that clarify the differences in soil properties between the vegetative types and between the timing of soil sampling. The PC loadings suggested that the first PC was the component that indicates total fertility of soil in the site, while the fifth PC indicates the dry to wet seasonal transition. The first PC was named the total fertility component (TFC). The linear regression between the TFC score and recently proposed indexes, the soil fertility index (SFI) or the soil evaluation factor (SEF), was highly significant (p < 0.001), indicating that the SFI and the SEF are applicable to measuring total fertility of soils in the SERS.     

Reproduction and larval development in three scalpellid barnacles, Scalpellum scalpellum (Linnaeus 1767), Ornatoscalpellum stroemii (M. Sars 1859) and Arcoscalpellum michelottianum (Seguenza 1876), Crustacea: Cirripedia: Thoracica): implications for reproduction and dispersal in the deep sea

We studied reproduction and larval development in three species of pedunculated barnacles with different depth distribution, that is, Scalpellum scalpellum (30–200 m), Ornatoscalpellum stroemii (100–1,600 m) and Arcoscalpellum michelottianum (64–5,190 m). Morphology, position and number of males in the female/hermaphrodite, type of larval development and the number and size of eggs were recorded. All three species have a pair of pocket-like receptacles, each of which can host only a single male in O. stroemii, up to five males in S. scalpellum and up to 12 males in A. michelottianum. Eggs and larvae were smallest in S. scalpellum, intermediately sized in O. stroemii and largest in A. michelottianum. Brood size was comparable for S. scalpellum and O. stroemii, but five times higher in A. michelottianum. The ratio for body/egg size is almost similar in S. scalpellum and A. michelottianum, but much smaller in O. stroemii. Both S. scalpellum and A. michelottianum have nauplii that spend upwards of 10 days in the plankton while the larvae of O. stroemii hatch as cyprids that settle soon after release. All these reproductive data indicate that O. stroemii invests considerably more in each propagule than the other two species. We hypothesize that the observed differences in reproductive system and mode of development in the three species represent adaptations to their different habitats. S. scalpellum are mainly transported by currents in the coastal sublittoral zone. O. stroemii is presumably spread by intermediate deep currents along the shelf and shelf-slope, while A. michelottianum occurs on seamounts and is probably transported by demersal currents over wide areas of inhospitable soft-bottoms. Our observations are in accordance with the general pattern that, egg-size and propagule-size are positively correlated to bathymetric and geographic distribution, and that the continental slope environment represents a high disturbance environment, where a short larval stage is an advantage.