Improving occupancy estimation when two types of observational error occur: non-detection and species misidentification

Efforts to draw inferences about species occurrence frequently account for false negatives, the common situation when individuals of a species are not detected even when a site is occupied. However, recent studies suggest the need to also deal with false positives, which occur when species are misidentified so that a species is recorded as detected when a site is unoccupied. Bias in estimators of occupancy, colonization, and extinction can be severe when false positives occur. Accordingly, we propose models that simultaneously account for both types of error. Our approach can be used to improve estimates of occupancy for study designs where a subset of detections is of a type or method for which false positives can be assumed to not occur. We illustrate properties of the estimators with simulations and data for three species of frogs. We show that models that account for possible misidentification have greater support (lower AIC for two species) and can yield substantially different occupancy estimates than those that do not. When the potential for misidentification exists, researchers should consider analytical techniques that can account for this source of error, such as those presented here.     

Estimating the abundance of mouse populations of known size: promises and pitfalls of new methods.

Knowledge of animal abundance is fundamental to many ecological studies. Frequently, researchers cannot determine true abundance, and so must estimate it using a method such as mark-recapture or distance sampling. Recent advances in abundance estimation allow one to model heterogeneity with individual covariates or mixture distributions and to derive multimodel abundance estimators that explicitly address uncertainty about which model parameterization best represents truth. Further, it is possible to borrow information on detection probability across several populations when data are sparse. While promising, these methods have not been evaluated using mark-recapture data from populations of known abundance, and thus far have largely been overlooked by ecologists. In this paper, we explored the utility of newly developed mark-recapture methods for estimating the abundance of 12 captive populations of wild house mice (Mus musculus). We found that mark-recapture methods employing individual covariates yielded satisfactory abundance estimates for most populations. In contrast, model sets with heterogeneity formulations consisting solely of mixture distributions did not perform well for several of the populations. We show through simulation that a higher number of trapping occasions would have been necessary to achieve good estimator performance in this case. Finally, we show that simultaneous analysis of data from low abundance populations can yield viable abundance estimates.     

Assessment of heavy metals in water samples and tissues of edible fish species from Awassa and Koka Rift Valley Lakes, Ethiopia

The Ethiopian Rift Valley Lakes host populations of edible fish species including Oreochromis niloticus, Labeobarbus intermedius and Clarias gariepinus, which are harvested also in other tropical countries. We investigated the occurrence of six heavy metals in tissues of these fish species as well as in the waters of Lake Koka and Lake Awassa. Both lakes are affected by industrial effluents in their catchments, making them ideal study sites. Mercury concentrations were very low in the water samples, but concentrations in the fish samples were relatively high, suggesting a particularly high bioaccumulation tendency as compared with the other investigated metals. Mercury was preferentially accumulated in the fish liver or muscle. It was the only metal with species-specific accumulation with highest levels found in the predatory species L. intermedius. Lower mercury concentrations in O. niloticus could be attributed to the lower trophic level, whereas mercury values in the predatory C. gariepinus were unexpectedly low. This probably relates to the high growth rate of this species resulting in biodilution of mercury. Accumulation of lead, selenium, chromium, arsenic and cadmium did not differ between species, indicating that these elements are not biomagnified in the food chain. Values of cadmium, selenium and arsenic were highest in fish livers, while lead and chromium levels were highest in the gills, which could be related to the uptake pathway. A significant impact of the industrial discharges on the occurrence of metals in the lakes could not be detected, and the respective concentrations in fish do not pose a public health hazard.     

Levels of organochlorine pesticides in Amazon turtle (Podocnemis unifilis) in the Xingu River,Brazil

Abstract

Due to the toxicity and high environmental persistence of organochlorine pesticides in aquatic organisms, turtles have been studied as environment biomonitors. These animals are important sources of protein for the riverside and indigenous peoples of the Brazilian amazon. In the present study, organochlorine pesticide contamination was investigated in Podocnemis unifilis. Liver, muscle and fatty tissue samples were removed from 50 specimens collected from five sampling points located in the Xingu River basin. Fourteen organochlorine pesticides were analysed via gas chromatography with an electron capture detector (CG-ECD). Eight organochlorine pesticides were detected with average concentrations of ∑DDT, ∑Endossulfan and ∑HCH which were 26.17?±?26.35, 14.38?±?23.77 and 1.39?±?8.46?ng g^?1 in moisture content, respectively. DDT compounds were the most predominant, with a greater concentration of pp′-DDT in the liver and pp′-DDD in the muscle. Significant differences were noted between the types of tissues studied, and the concentration of OCPs varied between sampling sites.     

The Effects of Three Chemical Algaecides on Cell Numbers and Toxin Content of the Cyanobacteria Microcystis aeruginosa and Anabaenopsis sp.

Toxic cyanobacteria blooms are a growing concern for public health and safety, due in part to the production of the hepatotoxin microcystin by certain species, including Microcystis aeruginosa. Management strategies for controlling cyanobacteria blooms include algaecide treatments, often with copper sulfate, and more recently oxidizers such as sodium percarbonate that produce hydrogen peroxide. This study assessed the effects of two copper-containing algaecides and one sodium percarbonate-containing algaecide on mitigating cell numbers and toxin content of cultured M. aeruginosa and summer (July) bloom samples of Anabaenopsis sp. in a brackish stormwater detention pond. Monitoring of the bloom revealed that Anabaenopsis sp. was associated with elevated levels of orthophosphate compared to nitrogen (dissolved inorganic nitrogen to phosphorus ratios were 0.19–1.80), and the bloom decline (September–October) was likely due to lower autumn water temperatures combined with potential grazing by the dinoflagellate Protoperidinium quinquecorne. Laboratory-based algaecide experiments included three dose levels, and cyanobacteria cell numbers and microcystin concentrations (particulate and dissolved) were evaluated over 7 d. Following exposure, copper-containing treatments generally had lower cell numbers than either sodium percarbonate-containing or control (no algaecide) treatments. Addition of algaecides did not reduce overall microcystin levels, and a release of toxin from the particulate to dissolved phase was observed in most treatments. These findings indicate that algaecide applications may visibly control cyanobacteria bloom densities, but not necessarily toxin concentrations, and have implications for public health and safety.     

Colonization and extinction in dynamic habitats: an occupancy approach for a Great Plains stream fish assemblage

Despite the importance of habitat in determining species distribution and persistence, habitat dynamics are rarely modeled in studies of metapopulations. We used an integrated habitat-occupancy model to simultaneously quantify habitat change, site fidelity, and local colonization and extinction rates for larvae of a suite of Great Plains stream fishes in the Arikaree River, eastern Colorado, USA, across three years. Sites were located along a gradient of flow intermittency and groundwater connectivity. Hydrology varied across years: the first and third being relatively wet and the second dry. Despite hydrologic variation, our results indicated that site suitability was random from one year to the next. Occupancy probabilities were also independent of previous habitat and occupancy state for most species, indicating little site fidelity. Climate and groundwater connectivity were important drivers of local extinction and colonization, but the importance of groundwater differed between periods. Across species, site extinction probabilities were highest during the transition from wet to dry conditions (range: 0.52-0.98), and the effect of groundwater was apparent with higher extinction probabilities for sites not fed by groundwater. Colonization probabilities during this period were relatively low for both previously dry sites (range: 0.02-0.38) and previously wet sites (range: 0.02-0.43). In contrast, no sites dried or remained dry during the transition from dry to wet conditions, yielding lower but still substantial extinction probabilities (range: 0.16-0.63) and higher colonization probabilities (range: 0.06-0.86), with little difference among sites with and without groundwater. This approach of jointly modeling both habitat change and species occupancy will likely be useful to incorporate effects of dynamic habitat on metapopulation processes and to better inform appropriate conservation actions.     

Industrial organic contaminants: identification,toxicity and fate in the environment

Industrialization and urbanization in the more economically developed countries and also in emerging and developing nations have led to an intensive and still increasing use of water resources. The involved chemical contamination led to a deterioration of aquatic systems in many areas. Industries are important pollution sources and the discharged wastewaters may contain very diverse and potentially harmful organic compound groups. We therefore present here a comprehensive review of the current state of knowledge of organic contaminants from industrial wastewaters. The available studies proved the heterogenic chemical composition of industrial wastewaters, even from the same industry branches, and the presence of heterogenic organic contaminant mixtures from industrial sources in aquatic systems. We conclude that our knowledge of the chemical composition of industrial wastewaters and the occurrence of industrial organic contaminants in the environment is as yet very limited. A combination of chemical and toxicological methods enabled the identification of toxic organic constituents in industrial wastewaters. Chemical evaluations of industrial contamination linked to surveys of environmental impacts could relate toxic effects of field samples to the presence of specific contaminants. Exposure experiments in the field proved the bioaccumulation and toxicity of several industrial compounds. Ecological surveys in industrial areas combined with a comprehensive chemical characterization and toxicity evaluation are so far missing. Some of the identified organic contaminants are related to characteristic industrial production processes, and their presence in water, sediment or biota indicates the input of specific industrial wastewaters. Accordingly, these compounds can be used as industrial markers. We suggest the proceeding application of the marker concept, as markers are useful to verify the input of specific industrial wastewaters to aquatic systems and to investigate the spatial distribution of the emission. Such information helps to disentangle different emission sources for the subsequent investigation of potential impacts in the environment.     

Literature review on risky driving videos on YouTube: Unknown effects and areas for concern?

Objective: Entry of terms reflective of extreme risky driving behaviors into the YouTube website yields millions of videos. The majority of the top 20 highly subscribed automotive YouTube websites are focused on high-performance vehicles, high speed, and often risky driving. Moreover, young men are the heaviest users of online video sharing sites, overall streaming more videos, and watching them longer than any other group. The purpose of this article is to review the literature on YouTube videos and risky driving.

Methods: A systematic search was performed using the following specialized database sources—Scopus, PubMed, Web of Science, ERIC, and Google Scholar—for the years 2005–2015 for articles in the English language. Search words included “YouTube AND driving,” “YouTube AND speeding,” “YouTube AND racing.”

Results: No published research was found on the content of risky driving videos or on the effects of these videos on viewers. This literature review presents the current state of our published knowledge on the topic, which includes a review of the effects of mass media on risky driving cognitions; attitudes and behavior; similarities and differences between mass and social media; information on the YouTube platform; psychological theories that could support YouTube's potential effects on driving behavior; and 2 examples of risky driving behaviors (“sidewalk skiing” and “ghost riding the whip”) suggestive of varying levels of modeling behavior in subsequent YouTube videos.

Conclusions: Every month about 1 billion individuals are reported to view YouTube videos (ebizMBA Guide 2015 ebizMBA Guide. Top 15 most popular websites. 2015. Available at: http://www.ebizmba.com/articles/most-popular-websites [Google Scholar]) and young men are the heaviest users, overall streaming more YouTube videos and watching them longer than women and other age groups (Nielsen 2011 Nielsen. State of the media: the social media report. Q3. 2011. Available at: http://www.nielsen.com/us/en/insights/reports/2011/social-media-report-q3.html [Google Scholar]). This group is also the most dangerous group in traffic, engaging in more per capita violations and experiencing more per capita injuries and fatalities (e.g., Parker et al. 1995 Parker D, Reason J, Manstead ASR, Stradling SG. Driving errors, driving violations and accident involvement. Ergonomics. 1995;38:1036–1048.[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]; Reason et al. 1990 Reason J, Manstead A, Stradling S, Baxter J, Campbell K. Errors and violations on the roads: a real distinction? Ergonomics. 1990;33:1315–1332.[Taylor &; Francis Online], [Web of Science ®] , [Google Scholar]; Transport Canada 2015 Vingilis E, Yilderim-Yenier Z, Fischer P, et al. Self-concept as a risky driver: Mediating the relationship between racing video games and on-road driving violations in a community-based sample. Transp Res Part F Traffic Psychol Behav. 2016;43:15–23. [Google Scholar]; World Health Organization 2015 World Health Organization. Road traffic injuries. Fact sheet no. 358. 2015. Available at: http://www.who.int/mediacentre/factsheets/fs358/en/# Accessed March 14, 2016. [Google Scholar]). YouTube also contains many channels depicting risky driving videos. The time has come for the traffic safety community to begin exploring these relationships.     

Using multilevel spatial models to understand salamander site occupancy patterns after wildfire

Studies of the distribution of elusive forest wildlife have suffered from the confounding of true presence with the uncertainty of detection. Occupancy modeling, which incorporates probabilities of species detection conditional on presence, is an emerging approach for reducing observation bias. However, the current likelihood modeling framework is restrictive for handling unexplained sources of variation in the response that may occur when there are dependence structures such as smaller sampling units that are nested within larger sampling units. We used multilevel Bayesian occupancy modeling to handle dependence structures and to partition sources of variation in occupancy of sites by terrestrial salamanders (family Plethodontidae) within and surrounding an earlier wildfire in western Oregon, USA. Comparison of model fit favored a spatial N-mixture model that accounted for variation in salamander abundance over models that were based on binary detection/non-detection data. Though catch per unit effort was higher in burned areas than unburned, there was strong support that this pattern was due to a higher probability of capture for individuals in burned plots. Within the burn, the odds of capturing an individual given it was present were 2.06 times the odds outside the burn, reflecting reduced complexity of ground cover in the burn. Ther was weak support that true occupancy was lower within the burned area. While the odds of occupancy in the burn were 0.49 times the odds outside the burn among the five species, the magnitude of variation attributed to the burn was small in comparison to variation attributed to other landscape variables and to unexplained, spatially autocorrelated random variation. While ordinary occupancy models may separate the biological pattern of interest from variation in detection probability when all sources of variation are known, the addition of random effects structures for unexplained sources of variation in occupancy and detection probability may often more appropriately represent levels of uncertainty.