A new procedure to optimize the selection of groups in a classification tree: Applications for ecological data

Agglomerative cluster analyses encompass many techniques, which have been widely used in various fields of science. In biology, and specifically ecology, datasets are generally highly variable and may contain outliers, which increase the difficulty to identify the number of clusters. Here we present a new criterion to determine statistically the optimal level of partition in a classification tree. The criterion robustness is tested against perturbated data (outliers) using an observation or variable with values randomly generated. The technique, called Random Simulation Test (RST), is tested on (1) the well-known Iris dataset [Fisher, R.A., 1936. The use of multiple measurements in taxonomic problems. Ann. Eugenic. 7, 179–188], (2) simulated data with predetermined numbers of clusters following Milligan and Cooper [Milligan, G.W., Cooper, M.C., 1985. An examination of procedures for determining the number of clusters in a data set. Psychometrika 50, 159–179] and finally (3) is applied on real copepod communities data previously analyzed in Beaugrand et al. [Beaugrand, G., Ibanez, F., Lindley, J.A., Reid, P.C., 2002. Diversity of calanoid copepods in the North Atlantic and adjacent seas: species associations and biogeography. Mar. Ecol. Prog. Ser. 232, 179–195]. The technique is compared to several standard techniques. RST performed generally better than existing algorithms on simulated data and proved to be especially efficient with highly variable datasets.     

Path selection and foraging efficiency in Argentine ant transport networks

We experimentally investigated both individual and collective behavior of the Argentine ant Linepithema humile as they crossed symmetrical and asymmetrical bifurcations in gallery networks. Ants preferentially followed the branch that deviated the least from their current direction and their probability to perform a U-turn after a bifurcation increased with the turning angle at the bifurcation. At the collective level, colonies were better able to find the shortest path that linked the nest to a food source in a polarized network where bifurcations were symmetrical from one direction and asymmetrical from the other than in a network where all bifurcations were symmetrical. We constructed a model of individual behavior and showed that an individual’s preference for the least deviating path will be amplified via the ants’ mass recruitment mechanism thus explaining the difference found between polarized and non-polarized networks. The foraging efficiency measured in the simulations was three times higher in polarized than in non-polarized networks after only 15 min. We conclude that measures of transport network efficiency must incorporate both the structural properties of the network and the behavior of the network users.     

Chemistry and aerosols in the marine boundary layer: 1-D modelling of the three ACE-2 Lagrangian experiments

Three Lagrangian experiments were conducted during IGAC's second aerosol characterization experiment (ACE-2) in the area between Portugal, Tenerife and Madeira in June/July 1997. During each Lagrangian experiment, a boundary layer air mass was followed for about 30 h, and the temporal evolution of its chemical and aerosol composition was documented by a series of vertical profiles and horizontal box pattern flown by the Meteorological Research Flight research aircraft Hercules C130. The wealth of observational data that has been collected during these three Lagrangian experiments is the basis for the development and testing of a one-dimensional Lagrangian boundary layer model with coupled gas, aqueous, and aerosol phase chemistry. The focus of this paper is on current model limitations and strengths. We show that the model is able to represent the dynamical and chemical evolution of the marine boundary layer, in some cases requiring adjustments of the subsidence velocity and of the surface heat fluxes. Entrainment of a layer rich in ozone and carbon monoxide from a residual continental boundary layer into the marine boundary layer as well as in-cloud oxidation of sulphur dioxide by hydrogen peroxide are simulated, and coherent results are obtained, concerning the evolution of the small, presumably sulphate–ammonia aerosol mode.     

International cross-validation of a BOD5 surrogate

BOD5 dates back to 1912 when the Royal Commission decided to use the mean residence time of water in the rivers of England, 5 days, as a standard to measure the biochemical oxygen demand. Initially designed to protect the quality of river waters from extensive sewage discharge, the use of BOD5 has been quickly extended to waste water treatment plants (WWTPs) to monitor their efficiency on a daily basis. The measurement has been automatized but remains a tedious, time- and resource-consuming analysis. We have cross-validated a surrogate BOD5 method on two sites in France and in the USA with a total of 109 samples. This method uses a fluorescent redox indicator on a 96-well microplate to measure microbial catabolic activity for a large number of samples simultaneously. Three statistical tests were used to compare surrogate and reference methods and showed robust equivalence.     

Challenges of soil mixing using catalyzed hydrogen peroxide with rotating dual axis blending technology

Although known to be one of the most effective oxidants for treatment of organic contaminants, catalyzed hydrogen peroxide (CHP) is typically not used for soil mixing applications because of health and safety concerns related to vapor generation and very rapid rates of reaction in open excavations. In likely the first large‐scale in situ CHP soil mixing application, an enhanced CHP, modified Fenton's reagent (MFR), was applied during soil mixing at the Kearsarge Metallurgical Superfund Site in New Hampshire. An innovative rotating dual‐axis blender (DAB) technology was used to safely mix the MFR into low‐plasticity silt and clay soils to remediate residual 1,1,1‐trichloroethane (111TCA); 1,1‐dichloroethene (11DCE); and 1,4‐dioxane (14D). It was expected that the aggressive treatment approach using relatively “greener” hydrogen peroxide (HP) chemistry would effectively treat Site contaminants without significant byproduct impacts to groundwater or the adjacent pond. The remediation program was designed to treat approximately 3,000 cubic yards of residual source area soil in situ by aggressively mixing MFR into the soils. The subsurface interval treated was from 7 to 15 feet below ground surface. To accurately track the soil mixing process and MFR addition, the Site was divided into 109 10‐foot square treatment cells that were precisely located, dosed, and mixed using the DAB equipped with an on‐board GPS system. The use of stabilizing agents along with careful calculation of the peroxide dose helped to ensure vapor‐free conditions in the vicinity of the soil mixing operation. Real‐time sampling and monitoring were critical in identifying any posttreatment exceedences of the cleanup goals. This allowed retreatment and supplemental testing to occur without impacting the soil mixing/in situ chemical oxidation (ISCO) schedule. Posttreatment 24‐hr soil samples were collected from 56 random locations after ensuring that the HP had been completely consumed. The posttreatment test results showed that 111TCA and 11DCE concentrations were reduced to nondetect (ND) or below the cleanup goals of 150 μg/kg for 111TCA and 60 μg/kg for 11DCE. Supplemental posttreatment soil samples, collected six months after treatment, showed 100 percent compliance with the soil treatment goals. Groundwater samples collected one year after the MFR soil mixing treatment program showed either ND or low concentrations for 111TCA, 11DCE, and 14D. Successful stabilization and site restoration was performed after overcoming considerable challenges associated with loss of soil structure, high liquid content, and reduced bearing capacity of the blended soils.     

Illegal trade in wild cats and its link to Chinese-led development in Central and South America

Seizures of hundreds of jaguar heads and canines in Central and South America from 2014 to 2018 resulted in worldwide media coverage suggesting that wildlife traffickers are trading jaguar body parts as substitutes for tiger parts to satisfy the demand for traditional Asian medicine. We compiled a data set of >1000 seized wild cats (jaguar [Panthera onca], puma [Puma concolor], and ocelot [Leopardus pardalis]) from 19 Central and South American countries and China. We ran generalized additive mixed models to detect trends in wild-cat seizures from 2012 to 2018 and assess the effects of socioeconomic factors of source countries and between those countries and China on the number of wild cats seized. Jaguar seizures increased over time, and most of the seized jaguar pieces were canines (1991 of 2117). Around 34% (32 of 93) of the jaguar-part seizure reports were linked with China, and these seizures contained 14-fold more individuals than those intended for domestic markets. Source countries with relatively high levels of corruption and Chinese private investment and low income per capita had 10–50 times more jaguar seizures than the remaining sampled countries. The number of Chinese residents in Central and South America was not significantly related to the number of jaguars seized. No socioeconomic factors influenced the seizures of puma and ocelots. Legal market chains may provide structure for the illegal chain; thus, the influx of illegal jaguar products is potentially a side effect of the economic partnership between Central and South American countries and China. Poverty and high levels of corruption in the source countries may motivate local people to engage in illegal activities and contribute to the growth of this trade. Supply-side interventions to curb this threat to Neotropical wild cats may include improved training for officials and promotion of governance and the value of protecting these animals to local people.     

Trends in Soil Erosion and Woody Shrub Encroachment in Ngqushwa District,Eastern Cape Province,South Africa

Woody shrub encroachment severely impacts on the hydrological and erosion response of rangelands and abandoned cultivated lands. These processes have been widely investigated at various spatial scales, using mostly field experimentation. The present study used remote sensing to investigate spatial and temporal patterns of soil erosion and encroachment by a woody shrub species, Pteronia incana, in a catchment in Ngqushwa district, Eastern Cape Province, South Africa between 1998 and 2008. The extreme categories of soil erosion and shrub encroachment were mapped with higher accuracy than the intermediate ones, particularly where lower spatial resolution data were used. The results showed that soil erosion in the worst category increased simultaneously with dense woody shrub encroachment on the hill slopes. This trend is related to the spatial patterning of woody shrub vegetation that increases bare soil patches—leading to runoff connectivity and concentration of overland flow. The major changes in soil erosion and shrub encroachment analysed during the 10-year period took place in the 5–9° slope category and on the concave slope form. Multi-temporal analyses, based on remote sensing, can extend our understanding of the dynamics of soil erosion and woody shrub encroachment. They may help benchmark the processes and assist in upscaling field studies.     

The Steubenville Comprehensive Air Monitoring Program (SCAMP): Concentrations and Solubilities of PM2.5 Trace Elements and Their Implications for Source Apportionment and Health Research

Abstract

The elemental compositions of the water-soluble and acid-digestible fractions of 24-hr integrated fine particulate matter (PM_2.5) samples collected in Steubenville, OH, from 2000 to 2002 were determined using dynamic reaction cell inductively coupled plasma-mass spectrometry. The water-soluble elemental compositions of PM_2.5 samples collected at four satellite monitoring sites in the surrounding region were also determined. Fe was the most abundant but least water soluble of the elements determined at the Steubenville site, having a mean ambient concentration of 272 µg/m³ and a median fractional solubility of 6%. Fe solubility and its correlations with SO₄ ^2? and temperature varied significantly by season, consistent with the hypothesis that secondary sulfates may help to mobilize soluble Fe under suitable summertime photochemical conditions. Significantly higher ambient concentrations were observed at Steubenville than at each of the four satellite sites for 10 of the 18 elements (Al, As, Ca, Cd, Fe, Mg, Mn, Na, Pb, and Zn) determined in the water-soluble PM_2.5 fraction. Concentrations of Fe, Mn, and Zn at Steubenville were substantially higher than concentrations reported recently for larger U.S. cities. Receptor modeling identified seven sources affecting the Steubenville site. An (NH₄)₂SO₄-dominated source, likely representing secondary PM_2.5 from coal-fired plants to the west and southwest of Steubenville, accounted for 42% of the PM_2.5 mass, and two sources likely dominated by emissions from motor vehicles and from iron and steel facilities in the immediate Steubenville vicinity accounted for 20% and 10%, respectively. Other sources included an NH₄NO₃ source (15%), a crustal source (6%), a mixed nonferrous metals and industrial source (3%), and a primary coal combustion source (3%). Results suggest the importance of very different regional and local source mechanisms in contributing to PM_2.5 mass at Steubenville and reinforce the need for further research to elucidate whether metals such as Fe, Mn, and Zn play a role in the PM_2.5 health effects observed previously there.     

The Role of Ethnobotanical Skills and Agricultural Labor in Forest Clearance: Evidence from the Bolivian Amazon

Research on the benefits of local ecological knowledge for conservation lacks empirical data on the pathways through which local knowledge might affect natural resources management. We test whether ethnobotanical skills, a proxy for local ecological knowledge, are associated to the clearance of forest through their interaction with agricultural labor. We collected information from men in a society of gatherers–horticulturalist, the Tsimane’ (Bolivia). Data included a baseline survey, a survey of ethnobotanical skills (n = 190 men), and two surveys on agricultural labor inputs (n = 466 plots). We find a direct effect of ethnobotanical skills in lowering the extent of forest cleared in fallow but not in old-growth forest. We also find that the interaction between ethnobotanical skills and labor invested in shifting cultivation has opposite effects depending on whether the clearing is done in old-growth or fallow forest. We explain the finding in the context of Tsimane’ increasing integration to the market economy.     

Alkane biodegradation and dynamics of phylogenetic subgroups of sulfate-reducing bacteria in an anoxic coastal marine sediment artificially contaminated with oil

For 503 days, unoiled control and artificially oiled sediments were incubated in situ at 20m water depth in a Mediterranean coastal area. Degradation of the aliphatic fraction of the oil added was followed by GC-MS. At the same time, terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA encoding genes was used to detect dynamics in the sulfate-reducing bacteria (SRB) community in response to the oil contamination. Specific polymerase chain reaction (PCR) primer sets for five generic or suprageneric groups of SRB were used for PCR amplification of DNA extracted from sediments. During the experiment, hydrocarbons from C(17) to C(30) were significantly degraded even in strictly anoxic sediment layers. Of the five SRB groups, only two groups were detected in the sediments (control and oiled), namely the Desulfococcus-Desulfonema-Desulfosarcina-like group and the Desulfovibrio-Desulfomicrobium-like group. Statistical analysis of community patterns revealed dynamic changes over time within these two groups following the contamination. Significant differences in community patterns were recorded in artificially oiled compared with control sediments. Cloning and sequencing of 16S rRNA encoding genes performed after 503 days showed that many of the most abundant sequences were closely related to hydrocarbonoclastic SRB which could have played an active role in the observed biodegradation of aliphatic hydrocarbons. Results from the present study provide useful information on the dynamics of dominant SRB in heavily oil-contaminated sediments and their potential for anaerobic biodegradation for the treatment of spilled oil in anoxic marine environments.