The fire frequency analysis branch of the pyrostatistics tree: sampling decisions and censoring in fire interval data

Statistical characterization of past fire regimes is important for both the ecology and management of fire-prone ecosystems. Survival analysis—or fire frequency analysis as it is often called in the fire literature—has increasingly been used over the last few decades to examine fire interval distributions. These distributions can be generated from a variety of sources (e.g., tree rings and stand age patterns), and analysis typically involves fitting the Weibull model. Given the widespread use of fire frequency analysis and the increasing availability of mapped fire history data, our goal has been to review and to examine some of the issues faced in applying these methods in a spatially explicit context. In particular, through a case study on the massive Cedar Fire in 2003 in southern California, we examine sensitivities of parameter estimates to the spatial resolution of sampling, point- and area-based methods for assigning sample values, current age surfaces versus historical intervals in generating distributions, and the inclusion of censored (i.e., incomplete) observations. Weibull parameter estimates were found to be roughly consistent with previous fire frequency analyses for shrublands (i.e., median age at burning of ~30–50 years and relatively low age dependency). Results indicate, however, that the inclusion or omission of censored observations can have a substantial effect on parameter estimates, far more than other decisions about specifics of sampling.

Genotoxic effects of Ag2S and CdS nanoparticles in blue mussel (Mytilus edulis) haemocytes

The use of functionalised metal sulphide nanoparticles (NPs) for nanoremediation and biomedical application is rapidly increasing, which could lead to significant inputs into the marine environment. The potential impact of some NPs on marine organisms is still poorly understood. In the present paper the genotoxic potential of Ag₂S and CdS NPs on Mytilus edulis haemocytes was assessed. MPEG-SH (thiol-terminated methyl polyethylene glycol), was used as capping agent to avoid NPs agglomeration. TEM analysis showed that the Ag₂S NPs size was 13±7 nm, whereas CdS quantum dots had an average diameter of 4±1 nm. DNA integrity was evaluated by Comet assay following exposure to increasing concentration series (0.01–10 mg/L). Both silver and cadmium NPs showed genotoxic effects at the highest dose. MPEG-SH was also found to exert a weak genotoxic activity, suggesting that at least part of the genotoxic potential of functionalised NPs on mussel cells might be attributable to the capping agent. These results confirm the genotoxic potential of Ag₂S NPs for mussel cells and demonstrated, for the first time, that CdS NPs is genotoxic in a marine organism.     

Environmental,social, morphological,and behavioral constraints on opportunistic multiple paternity

Multiple mating and multiple paternity in polytocous species have been mostly studied from an adaptive (i.e., cost–benefit) perspective. Disease, time, energy, and the risk of injuries are well-known costs of multiple mating, yet from both male and female perspectives, a number of genetic and non-genetic benefits have also been identified. The effects of environmental conditions and individual-specific behavior, however, are much less well understood. Using a long-term study on yellow-bellied marmots (Marmota flaviventris), we evaluated the impacts of environmental variation, social structure, female body mass, and female docility (a personality trait) on the occurrence of multiple paternity. Multiple paternity was influenced by environmental constraints, social constraints, a female’s personality, and her body mass at emergence from hibernation. Personality and mass effects were detected only when environmental or social conditions were favorable. Our results suggest that multiple paternity is mainly limited by the opportunity to have access to multiple mates and is influenced by costs or mate choice because heavier females were more likely to have litters with multiple sires than smaller ones. Future studies in other species might benefit from considering environmental constraints when studying multiple paternity.     

Hierarchical modeling of abundance in closed population capture–recapture models under heterogeneity

Hierarchical modeling of abundance in space or time using closed-population mark-recapture under heterogeneity (model \(\hbox {M}_{\text {h}}\) ) presents two challenges: (i) finding a flexible likelihood in which abundance appears as an explicit parameter and (ii) fitting the hierarchical model for abundance. The first challenge arises because abundance not only indexes the population size, it also determines the dimension of the capture probabilities in heterogeneity models. A common approach is to use data augmentation to include these capture probabilities directly into the likelihood and fit the model using Bayesian inference via Markov chain Monte Carlo (MCMC). Two such examples of this approach are (i) explicit trans-dimensional MCMC, and (ii) superpopulation data augmentation. The superpopulation approach has the advantage of simple specification that is easily implemented in BUGS and related software. However, it reparameterizes the model so that abundance is no longer included, except as a derived quantity. This is a drawback when hierarchical models for abundance, or related parameters, are desired. Here, we analytically compare the two approaches and show that they are more closely related than might appear superficially. We exploit this relationship to specify the model in a way that allows us to include abundance as a parameter and that facilitates hierarchical modeling using readily available software such as BUGS. We use this approach to model trends in grizzly bear abundance in Yellowstone National Park from 1986 to 1998.     

Using expert knowledge to support Endangered Species Act decision-making for data-deficient species

Many questions relevant to conservation decision-making are characterized by extreme uncertainty due to lack of empirical data and complexity of the underlying ecologic processes, leading to a rapid increase in the use of structured protocols to elicit expert knowledge. Published ecologic applications often employ a modified Delphi method, where experts provide judgments anonymously and mathematical aggregation techniques are used to combine judgments. The Sheffield elicitation framework (SHELF) differs in its behavioral approach to synthesizing individual judgments into a fully specified probability distribution for an unknown quantity. We used the SHELF protocol remotely to assess extinction risk of three subterranean aquatic species that are being considered for listing under the U.S. Endangered Species Act. We provided experts an empirical threat assessment for each known locality over a video conference and recorded judgments on the probability of population persistence over four generations with online submission forms and R-shiny apps available through the SHELF package. Despite large uncertainty for all populations, there were key differences between species’ risk of extirpation based on spatial variation in dominant threats, local land use and management practices, and species’ microhabitat. The resulting probability distributions provided decision makers with a full picture of uncertainty that was consistent with the probabilistic nature of risk assessments. Discussion among experts during SHELF's behavioral aggregation stage clearly documented dominant threats (e.g., development, timber harvest, animal agriculture, and cave visitation) and their interactions with local cave geology and species’ habitat. Our virtual implementation of the SHELF protocol demonstrated the flexibility of the approach for conservation applications operating on budgets and time lines that can limit in-person meetings of geographically dispersed experts.     

Improving species status assessments under the U.S. Endangered Species Act and implications for multispecies conservation challenges worldwide

Despite its successes, the U.S. Endangered Species Act (ESA) has proven challenging to implement due to funding limitations, workload backlog, and other problems. As threats to species survival intensify and as more species come under threat, the need for the ESA and similar conservation laws and policies in other countries to function efficiently has grown. Attempts by the U.S. Fish and Wildlife Service (USFWS) to streamline ESA decisions include multispecies recovery plans and habitat conservation plans. We address species status assessment (SSA), a USFWS process to inform ESA decisions from listing to recovery, within the context of multispecies and ecosystem planning. Although existing SSAs have a single-species focus, ecosystem-based research can efficiently inform multiple SSAs within a region and provide a foundation for transition to multispecies SSAs in the future. We considered at-risk grassland species and ecosystems within the southeastern United States, where a disproportionate number of rare and endemic species are associated with grasslands. To initiate our ecosystem-based approach, we used a combined literature-based and structured World Café workshop format to identify science needs for SSAs. Discussions concentrated on 5 categories of threats to grassland species and ecosystems, consistent with recommendations to make shared threats a focus of planning under the ESA: (1) habitat loss, fragmentation, and disruption of functional connectivity; (2) climate change; (3) altered disturbance regimes; (4) invasive species; and (5) localized impacts. For each threat, workshop participants identified science and information needs, including database availability, research priorities, and modeling and mapping needs. Grouping species by habitat and shared threats can make the SSA process and other planning processes for conservation of at-risk species worldwide more efficient and useful. We found a combination of literature review and structured discussion effective for identifying the scientific information and analysis needed to support the development of multiple SSAs. Article impact statement: Species status assessments can be improved by an ecosystem-based approach that groups imperiled species by shared habitats and threats.     

Ecological boundary detection using Bayesian areal wombling

The study of ecological boundaries and their dynamics is of fundamental importance to much of ecology, biogeography, and evolution. Over the past two decades, boundary analysis (of which wombling is a subfield) has received considerable research attention, resulting in multiple approaches for the quantification of ecological boundaries. Nonetheless, few methods have been developed that can simultaneously (1) analyze spatially homogenized data sets (i.e., areal data in the form of polygons rather than point-reference data); (2) account for spatial structure in these data and uncertainty associated with them; and (3) objectively assign probabilities to boundaries once detected. Here we describe the application of a Bayesian hierarchical framework for boundary detection developed in public health, which addresses these issues but which has seen limited application in ecology. As examples, we analyze simulated spread data and the historic pattern of spread of an invasive species, the hemlock woolly adelgid (Adelges tsugae), using county-level summaries of the year of first reported infestation and several covariates potentially important to influencing the observed spread dynamics. Bayesian areal wombling is a promising approach for analyzing ecological boundaries and dynamics related to changes in the distributions of native and invasive species.     

Differential deposition of antimicrobial proteins in blue tit (Cyanistes caeruleus) clutches by laying order and male attractiveness

Female birds can influence offspring fitness by varying the relative quantities of egg components they deposit within and between clutches. Antimicrobial proteins (lysozyme, ovotransferrin, and avidin) are significant components of the avian albumen and likely aid in defense of embryos from microbial infection. Within clutches, females may enhance antimicrobial defense of early-laid eggs to protect them from the high risk of infection incurred before the onset of incubation. Among entire clutches, females may invest more resources in young sired by more attractive males because they have higher reproductive value. We tested these hypotheses by quantifying antimicrobial protein distribution within and among clutches in blue tit eggs. Contrary to our hypothesis, clutches showed no differential deposition of lysozyme or avidin within clutches, but eggs laid in the middle of the sequence had higher concentrations of ovotransferrin than eggs in the beginning and end. Consistent with our second hypothesis, we found that females produced eggs with higher concentrations of lysozyme (although not ovotransferrin or avidin) when mated to more attractive (more UV-reflective) males. Furthermore, females mated to polygynous males deposited less lysozyme than those mated to monogamous males. These data suggest that allocation of lysozyme at the clutch level may be a maternal effect mediated by male qualities.     

Pilot study of personal, indoor and outdoor exposure to benzene, formaldehyde and acetaldehyde

There is a lack of data for health risk assessment of long term personal exposure to certain ubiquitous air pollutants present particularly in urban atmospheres. The relationship between ambient background concentrations and personal exposure is often unknown. A pilot campaign to measure indoor concentrations, outdoor concentrations and personal exposure to benzene, formaldehyde and acetaldehyde was conducted in a medium sized French town. A strong contribution to total personal exposure was observed from indoor sources, especially for formaldehyde and acetaldehyde, suggesting that indoor sources are dominant for these compounds. For benzene, the average personal exposure exceeded a 10 μgm^?3 limit value, although this was not the case for the ambient background concentration. For formaldehyde, the limit level was also exceeded. Observations suggest that true personal exposure cannot be determined directly from measurements pertaining from fixed ambient background monitoring stations. It is hoped that this will be taken into consideration by the bodies responsible for monitoring air pollution and the future European Air Quality Directive.     

Photo-Induced OH reactions of naphthalene and its oxidation products on SiO2

The photo-induced degradation of naphthalene, 1,4-naphthoquinone, 1-naphthol and 1-NO₂ naphthalene, adsorbed on silica gel, and with the addition of nitrogenous air pollutants e.g. NO₂ (as KNO₂) was investigated. Results indicate that compounds adsorbed onto a solid carrier are degraded when irradiated with UV light (λ > 290 nm) in the presence of nitrites. The key species initiating the naphthalene degradation is the OH-radical which is generated through the photolysis of NO₂. Reaction products identified were 2-formyl-cinnamaldehyde, 1,4-naphthoquinone, nitronaphthol, o-phthaldialdehyde, phthalide and nitronaphthalene. A mass balance between 40–50% was achieved. Under the same irradiation conditions, 1-NO₂ naphthalene is mainly degraded by direct photolysis while degradation of 1-naphthol and 1,4-naphthoquinone proceeds via the reaction with OH-radicals. Identified products were hydroxy-nitro-nitroso- and quinones compounds.