Jointly estimating survival and mortality: integrating recapture and recovery data from complex multiple predator systems

Environmental and Ecological Statistics - Identifying where, when, and how many animals live and die over time is principal to understanding factors that influence population dynamics....     

Nonparametric spatial regression of survival probability: visualization of population sinks in Eurasian woodcock

Both evolutionary ecologists and wildlife managers make inference based on how fitness and demography vary in space. Spatial variation in survival can be difficult to assess in the wild because (1) multisite study designs are not well suited to populations that are continuously distributed across a large area and (2) available statistical models accounting for detectability less than 1.0 do not easily cope with geographical coordinates. Here we use penalized splines within a Bayesian state-space modeling framework to estimate and visualize survival probability in two dimensions. The approach is flexible in that no parametric form for the relationship between survival and coordinates need be specified a priori. To illustrate our method, we study a game species, the Eurasian Woodcock Scolopax rusticola, based on band recovery data (5000 individuals) collected over a > 50 000-km2 area in west-central France with contrasted habitats and hunting pressures. We find that spatial variation in survival probability matches an index of hunting pressure and creates a mosaic of population sources and sinks. Such analyses could provide guidance concerning the spatial management of hunting intensity or could be used to identify pathways of spatial variation in fitness, for example, to study adaptation to changing landscape and climate.     

Participatory Bayesian network modeling to understand driving factors of land-use change decisions: insights from two case studies in northeast Madagascar

ABSTRACT

Forest frontiers worldwide reveal trade-offs that are key in mitigating global change. In the forest frontiers of northeast Madagascar, land-use changes result from decisions made by smallholder farmers. In the past, subsistence needs led to increasing shifting cultivation, resulting in forest degradation and deforestation. This study focuses on investigating the role of locally determined factors in land-use change decisions in the forest frontier context. Therefore, we developed a Bayesian network-based land-use decision model that represents the causalities between factors influencing land-use decisions and takes into account local decision-makers’ knowledge. The approach is applied in two comparative case studies in northeast Madagascar. Results show that farmers mostly aim at extending the cultivation of cash crops. These results and the causal mechanisms disentangled for the forest frontier of northeast Madagascar help understand change mechanisms and hence, support decision-making to attain the Sustainable Development Goals.     

Escape from UV threats in zooplankton: a cocktail of behavior and protective pigmentation

In order to avoid environmental threats, organisms may respond by altering behavior or phenotype. Using experiments performed in high-latitude Siberia and in temperate Sweden, we show for the first time that, among freshwater crustacean zooplankton, the defense against threats from ultraviolet radiation (UV) is a system where phenotypic plasticity and behavioral escape mechanisms function as complementary traits. Freshwater copepods relied mainly on accumulating protective pigments when exposed to UV radiation, but Daphnia showed strong behavioral responses. Pigment levels for both Daphnia and copepods were generally higher at higher latitudes, mirroring different UV threat levels. When released from the UV threat, Daphnia rapidly reduced (within 10 days) their UV protecting pigmentation-by as much as 40%--suggesting a cost in maintaining UV protective pigmentation. The evolutionary advantage of protective pigments is, likely, the ability to utilize the whole water column during daytime; conversely, since the amount of algal food is generally higher in surface waters, unpigmented individuals are restricted to a less preferred feeding habitat in deeper waters. Our main conclusion is that different zooplankton taxa, and similar taxa at different latitudes, use different mixes of behavior and pigments to respond to UV radiation.     

Biological and oceanographic insights from larval labrid (Pisces: Labridae) identification using mtDNA sequences

Polymerase chain reaction and direct comparison of mitochondrial DNA sequences from a cytochrome b gene fragment were used to identify two morphologically distinct larval types ofXyrichtys, a genus of tropical wrasse (Pisces: Labridae). Both larval types were collected during ichthyoplankton surveys on the Middle Atlantic Bight shelf in the summer of 1988. DNA sequence comparisons indicated that both types were larvae ofXyrichtys novacula (Linnaeus). Back-calculated birthdate distributions for those larvae collected on the Middle Atlantic Bight shelf demonstrated that the two larval types formed two distinct cohorts indicating a biological difference. The two distinct larval types may be a consequence of an ecophenotypic effect, or they may represent offspring from genetically distinct populations. These results emphasize that important biological and oceanographic information can be gained through the use of the polymerase chain reaction and DNA sequencing for larval identificaiton.     

Environmental information stored in otoliths: insights from stable isotopes

The present study compares the stable oxygen-and carbon-isotope ratios (¹⁸0:¹⁶O;¹³C:¹²C) in the otoliths of Atlantic cod,Gadus morhua, with those expected at equilibrium with seawater. Otoliths from juveniles reared for a 3 mo period under controlled conditions indicate that otoliths are formed in isotopic disequilibrium with seawater. This is probably due to positive metabolic fractionating of the heavier isotopes. This vital effect remains constant over the temperature range studied here (9 to 16°C) but may differ among other species. Our data indicate that the concentration of¹⁸O in calcium carbonate is inversely related to temperature and is described as ¹⁸O_a – _w – 3.79 – 0.200(T°C). The¹³C:¹²C ratios of otoliths and body tissues are related to the carbon ratio in the food source, although we found that the¹³C concentration is considerably higher in the otoliths relative te, the body tissues and the diet.     

Modelling habitat conversion in miombo woodlands: insights from Tanzania

Understanding the drivers of natural habitat conversion is a major challenge, yet predicting where future losses may occur is crucial to preventing them. Here, we used Bayesian analysis to model spatio-temporal patterns of land-use/cover change in two protected areas designations and unclassified land in Tanzania using time-series satellite images. We further investigated the costs and benefits of preserving fragmenting habitat joining the two ecosystems over the next two decades. We reveal that habitat conversion is driven by human population, existing land-use systems and the road network. We also reveal the probability of habitat conversion to be higher in the least protected area category. Preservation of habitat linking the two ecosystems saving 1640 ha of land from conversion could store between 21,320 and 49,200 t of carbon in the next 20 years, with the potential for generating between US$ 85,280 and 131,200 assuming a REDD+ project is implemented.     

A correction to: biological and oceanographic insights from larval labrid (Pisces: Labridae) identification using mtDNA sequences

Previously published mtDNA cytochrome b sequences for Xyrichtys novacula (Linnaeus) and two morphologically distinct types of Xyrichtys larvae (Pisces: Labridae) included human cytochrome b sequence, presumably due to sample contamination and/or poor preservation of sample DNA. Those sequences had been used to identify the two types of Xyrichtys larvae as X. novacula, but owing to the contamination, the identifications are invalid. Fresh specimens were collected: X.␣martinicensis (Cuvier and Valenciennes), X. novacula, X. splendens (Castelnau), and Xyrichtys sp. larvae of each of the two morphotypes (dorsal-forward eye and ventral-forward eye). The cytochrome b fragment was amplified from each specimen using the polymerase chain reaction. Comparison of the sequences with human cytochrome b sequence confirmed that the new sequences were not contaminated. The interspecific differences in Xyrichtys sequences were less than previously reported, but still greater than observed in many fish genera. Distance and parsimony analyses indicated that X. novacula and X. martinicensis were more closely related to each other than to X. splendens. This conclusion differs from our previous conclusion that X. martinicensis and X. splendens were more closely related to each other than to X. novacula. Distance and parsimony analyses also demonstrated that both larval morphotypes were X. novacula and, thus, our previous conclusions regarding larval ecology and oceanographic transport remain unchanged. Received: 12 March 1997 / Accepted: 24 October 1997     

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.

Occurrence of veterinary antibiotics in struvite recovery from swine wastewater by using a fluidized bed

Antibiotics in wastewater pose pharmacological threats to phosphorous recovery. Recovered struvite particles possessed significantly antibiotic residues. Smaller granules contained much more antibiotics than the larger ones. Organic matters and struvite granulation process exerted significant impacts. Recovering phosphorus from livestock wastewater has gained extensive attention. The residue of veterinary antibiotics in the wastewater may be present in the recovered products, thereby posing pharmacological threats to the agricultural planting and human health. This study investigated antibiotic occurrence in the struvite particles recovered from swine wastewater by using a fluidized bed. Results revealed that tetracyclines possessed significant residues in the struvite granules, with the values ranging from 195.2 mg·kg⁻¹ to 1995.0 mg·kg⁻¹. As for fluoroquinolones, their concentrations varied from 0.4 mg·kg⁻¹ to 1104.0 mg·kg⁻¹. Struvite particles were of various sizes and shapes and displayed different antibiotic adsorption capacities. The data also showed that the smaller granules contained much more antibiotics than the larger ones, indicating that the fluidized granulation process of struvite crystals plays an important role on the accumulation of antibiotics. For tetracyclines, organic matters and struvite adsorption exerted significant impacts on tetracyclines migration. The outcomes underscore the need to consider the residues of antibiotics in resource recovery from wastewater because they exert pharmacological impacts on the utilization of recovered products.     

When to come out from your own shell: risk-sensitive hiding decisions in terrapins

Animals should optimize the decision of when to come out from a refuge after a predators unsuccessful attack because hiding may be costly. Many prey run to hide in refuges in their habitat, whereas others are sessile and take refuge in a protective structure surrounding their body. An intermediate situation is when animals, such as turtles, have morphological structures that provide some partial protection, but they are also able to escape actively to safer refuges. This might complicate hiding decisions predicted by the theory of optimal-refuge use. We studied antipredatory tactics of Spanish terrapins (Mauremys leprosa) in response to simulated predatory attacks with different characteristics (i.e. combinations of several risk factors) and under different conditions (i.e. proximity to safe refuges), which should contribute to overall risk-level estimation. We specifically examined how risk level affected time spent withdrawn into the shell and time until turtles switched to an active escape tactic. The results showed that turtles were able to adjust their hiding behavior by assessing the risk of emerging before the predator had left the area. However, increasing hiding time may also increase the risk that the predator was able to injure or kill the turtle. Thus, the possibility of switching the antipredatory tactic to an alternative active escape to safer refuges (i.e. water) also influenced hiding times.Communicated by P. Bednekoff     

“NEW” resource recovery from wastewater using bioelectrochemical systems: Moving forward with functions

Bioelectrochemical systems (BES) have been extensively studied for resource recovery from wastewater. By taking advantage of interactions between microorganisms and electrodes, BES can accomplish wastewater treatment while simultaneously recovering various resources including nutrients, energy and water (“NEW”). Despite much progress in laboratory studies, BES have not been advanced to practical applications. This paper aims to provide some subjective opinions and a concise discussion of several key challenges in BES-based resource recovery and help identify the potential application niches that may guide further technological development. In addition to further increasing recovery efficiency, it is also important to have more focus on the applications of the recovered resources such as how to use the harvested electricity and gaseous energy and how to separate the recovered nutrients in an energy-efficient way. A change in mindset for energy performance of BES is necessary to understand overall energy production and consumption. Scaling up BES can go through laboratory scale, transitional scale, and then pilot scale. Using functions as driving forces for BES research and development will better guide the investment of efforts.

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Perceptions of incentives for participation: insights from joint forest management in India

The participatory approach in management of forests is now well established in forest policies of many developing countries. Incentives for different groups to participate have been argued by many to be desirable characteristics to promote participation. A key challenge for government and donor agencies is to develop better understanding of the incentives for different groups to be able to achieve and sustain their participation. Based on a case study of a joint forest management (JFM) programme in the northern state of Haryana in India, this paper highlights the relevance of understanding people's perception of the incentives. It specifically examines three hypotheses related to perceptions of villagers about incentives offered under the JFM programme and relates them to their participation in joint management. It concludes that a better understanding is likely to help in improving project implementation at the local level and the design of participatory forest management programmes more generally.     

Bioenergy recovery from landfill gas: A case study in China

Landfill gas (LFG) utilization which means a synergy between environmental protection and bioenergy recovery was investigated in this study. Pressure swing adsorption technology was used in LFG purification, and laboratory experiment, pilot-scale test, and on-site demonstration were carried out in Shenzhen, China. In the laboratory experiment, A-type carbon molecular sieve was selected as the adsorbent by comparison of several other adsorbents. The optimal adsorption pressure and adsorption time were 0.25 MPa and 2 min, respectively, under which the product generation rate was 4.5 m³/h and the methane concentration was above 90%. The process and optimization of the pilot-scale test were also reported in the paper. The product gas was of high quality compared with the National Standard of Compressed Natural Gas as Vehicle Fuel (GB18047-2000), when the air concentration in feed gas was under 10.96%. The demonstration project was composed of a collection system, production system, and utilization system. The drive performance, environmental protection performance, and economic feasibility of the product gas — as alternative fuel in passenger car, truck, and bulldozer—were tested, showing the feasibility technology for LFG utilization.     

Directing technical change from fossil-fuel to renewable energy innovation: An application using firm-level patent data

In this paper we provide an analysis of directed technical change in the sector of electricity generation. We rely on patent data in fossil-fuel (FF) and renewable energy (REN) technologies for 5471 European firms over the 1978–2006 period. The novelty of our approach is in the focus on firm׳s heterogeneity in driving technological change. We make a distinction between small specialized firms, which innovate in only one type of technology, and large mixed firms, which innovate in both technologies, to analyse how REN patents can replace FF ones at the sector level both through a shift in innovation activities within existing firms and through firms׳ entry and exit. We use zero-inflated count data estimation techniques to identify the factors that affect specialized versus mixed firms׳ patenting behaviour both at the intensive (i.e., levels of innovation) and extensive (i.e., technological entry) margins. We further investigate the implications of our firm-level estimations for reducing the gap between REN and FF innovation at the aggregate level. We establish two key findings: (1) a decrease in the FF-REN technology gap mainly comes about through technological entry of specialized REN firms following an increase in REN market size; (2) increases in FF prices, FF market size, and FF knowledge stocks all increase the technology gap by increasing mixed firms FF innovation rates. An important implication of our results is that policies aimed at increasing REN innovation should focus on helping small firms to start and sustain innovation in the long-run.     

Predicting richness effects on ecosystem function in natural communities: insights from high-elevation streams

. Despite the increased complexity of experimental and theoretical studies on the biodiversity-ecosystem functioning (B-EF) relationship, a major challenge is to demonstrate whether the observed importance of biodiversity in controlled experimental systems also persists in nature. Due to their structural simplicity and their low levels of human impacts, extreme species-poor ecosystems may provide new insights into B-EF relationships in natural systems. We address this issue using shredder invertebrate communities and organic matter decomposition rates in 24 high-altitude (3200-3900 m) Neotropical streams as a study model. We first assessed the effects of stream characteristics and shredder diversity and abundance on organic matter decomposition rates in coarse- and fine-mesh bags. We found the interaction term shredder richness x shredder abundance had the most significant impact on decomposition rates in the field, although water discharge may also play a role locally. We also examined the relative contribution of the three most abundant shredders on decomposition rates by manipulating shredder richness and community composition in a field experiment. Transgressive overyielding was detected among the three shredder species, indicating complementary resource use and/or facilitation. By integrating survey and experimental data in surface response analyses we found that observed B-EF patterns fit those predicted by a linear model that described litter decomposition rates as a function of increasing shredder richness and the relative abundance of the most efficient shredders. Finally, the validity of our approach was tested in a broader context by using two independent but comparable data sets from 49 French and Swedish streams showing more complex shredder community structure. Results revealed that richness and identity effects on decomposition rates were lost with increasing shredder community complexity. Our approach of combining experimental and empirical data with modeling in species-poor ecosystems may serve as an impetus for new B-EF studies. If theory can explain B-EF in low-diversity ecosystems, it may also have credibility in more complex ones.     

Hermaphroditism in brown shrimp: lessons from field data and modelling

This study was undertaken to further clarify whether the brown shrimp, Crangon crangon (Linnaeus 1758), is a gonochorist, a facultative or an obligate hermaphrodite. Juvenile shrimps were sampled from intertidal habitats along the German Wadden Sea coast with a push net and from a power plant water inlet to quantify the share of primary females. Length-based sex ratios were determined for about 27,000 individuals using external characteristics. Observed sex ratios were mainly female-biased, and also large males occurred regularly in the catch. This indicates that sex at hatch is not male as would be characteristic for an obligate protandric hermaphrodite and that not all male shrimps change sex. A cohort-based computer simulation, including sex-specific growth rates, mortality and seasonally varying recruitment, generated sex ratios comparable to the field. The observed decline in the proportion of males with increasing size can be explained solely by faster growth of females without involving hermaphroditism. Based on temperature-dependent growth and moult rates as well as length-specific numbers of eggs per female, the potential egg production of primary and secondary females was modelled, yielding contributions of secondary females of <1%. Sex change in C. crangon has previously been observed and may be interpreted as an evolutionary relict of this species having evolved in a habitat characterized by lower population densities, lower predation levels and increased longevity compared to today’s living conditions in North Sea coastal waters.     

Sexual segregation in distribution,diet and trophic level of seabirds: insights from stable isotope analysis

Considerable attention has focused on inter- and intraspecific variation in trophic niches of marine predators. Although this has revealed evidence for sexual segregation in distribution in some species, few studies have been able to address sex-related dietary specialisation. Stable isotope analysis of blood cells collected from albatrosses and petrels at South Georgia during chick-rearing indicated a difference in δ¹³C, suggesting that females fed to the north of males, only in two species with male-biased sexual size dimorphism; in no species did sexes differ in trophic level (δ¹⁵N). Based on a wider review, significant differences between sexes in isotope signatures were much more common in seabirds during the pre-laying or breeding than the nonbreeding period, presumably reflecting greater between-sex partitioning of resources when foraging ranges are more constrained and competition is greater. Sex differences, or their absence, were usually consistent across successive stages during the pre-laying and breeding periods, but not necessarily year-round nor between populations. Significant differences in isotope signatures between males and females were extremely rare in monomorphic species, suggesting a link between sexual size dimorphism and segregation in diet or distribution. Among the Southern Ocean albatrosses, sex differences in δ¹³C suggested the underlying mechanism was related to habitat specialisation, whereas in other size-dimorphic taxa (both male- and female-biased), sex differences were more common in δ¹⁵N than δ¹³C and therefore more consistent with size-mediated competitive exclusion or dietary specialisation.