Social network analysis and valid Markov chain Monte Carlo tests of null models

Analyses of animal social networks derived from group-based associations often rely on randomisation methods developed in ecology (Manly, Ecology 76:1109–1115, 1995) and made available to the animal behaviour community through implementation of a pair-wise swapping algorithm by Bejder et al. (Anim Behav 56:719–725, 1998). We report a correctable flaw in this method and point the reader to a wider literature on the subject of null models in the ecology literature. We illustrate the importance of correcting the method using a toy network and use it to make a preliminary analysis of a network of associations among eagle rays.

Animal social networks: an introduction

Network analysis has a long history in the mathematical and social sciences and the aim of this introduction is to provide a brief overview of the potential that it holds for the study of animal behaviour. One of the most attractive features of the network paradigm is that it provides a single conceptual framework with which we can study the social organisation of animals at all levels (individual, dyad, group, population) and for all types of interaction (aggressive, cooperative, sexual etc.). Graphical tools allow a visual inspection of networks which often helps inspire ideas for testable hypotheses. Network analysis itself provides a multitude of novel statistical tools that can be used to characterise social patterns in animal populations. Among the important insights that networks have facilitated is that indirect social connections matter. Interactions between individuals generate a social environment at the population level which in turn selects for behavioural strategies at the individual level. A social network is often a perfect means by which to represent heterogeneous relationships in a population. Probing the biological drivers for these heterogeneities, often as a function of time, forms the basis of many of the current uses of network analysis in the behavioural sciences. This special issue on social networks brings together a diverse group of practitioners whose study systems range from social insects over reptiles to birds, cetaceans, ungulates and primates in order to illustrate the wide-ranging applications of network analysis. This contribution is part of the special issue “Social Networks: new perspectives” (Guest Editors: J. Krause, D. Lusseau and R. James).     

Sustainable Use of Biotechnology for Bioenergy Feedstocks

Done correctly, cellulosic bioenergy should be both environmentally and economically beneficial. Carbon sequestration and decreased fossil fuel use are both worthy goals in developing next-generation biofuels. We believe that biotechnology will be needed to significantly improve yield and digestibility of dedicated perennial herbaceous biomass feedstocks, such as switchgrass and Miscanthus, which are native to the US and China, respectively. This Forum discusses the sustainability of herbaceous feedstocks relative to the regulation of biotechnology with regards to likely genetically engineered traits. The Forum focuses on two prominent countries wishing to develop their bioeconomies: the US and China. These two countries also share a political desire and regulatory frameworks to enable the commercialization and wide release of transgenic feedstocks with appropriate and safe new genetics. In recent years, regulators in both countries perform regular inspections of transgenic field releases and seriously consider compliance issues, even though the US framework is considered to be more mature and stringent. Transgene flow continues to be a pertinent environmental and regulatory issue with regards to transgenic plants. This concern is largely driven by consumer issues and ecological uncertainties. Regulators are concerned about large-scale releases of transgenic crops that have sexually compatible crops or wild relatives that can stably harbor transgenes via hybridization and introgression. Therefore, prior to the commercialization or extensive field testing of transgenic bioenergy feedstocks, we recommend that mechanisms that ensure biocontainment of transgenes be instituted, especially for perennial grasses. A cautionary case study will be presented in which a plant’s biology and ecology conspired against regulatory constraints in a non-biomass crop perennial grass (creeping bentgrass, Agrostis stolonifera), in which biocontainment was not attained. Appropriate technologies that could be applied to perennial grass feedstocks for biocontainment are discussed.     

The geographic distribution and economic value of climate change-related ozone health impacts in the United States in 2030

In this United States-focused analysis we use outputs from two general circulation models (GCMs) driven by different greenhouse gas forcing scenarios as inputs to regional climate and chemical transport models to investigate potential changes in near-term U.S. air quality due to climate change. We conduct multiyear simulations to account for interannual variability and characterize the near-term influence of a changing climate on tropospheric ozone-related health impacts near the year 2030, which is a policy-relevant time frame that is subject to fewer uncertainties than other approaches employed in the literature. We adopt a 2030 emissions inventory that accounts for fully implementing anthropogenic emissions controls required by federal, state, and/or local policies, which is projected to strongly influence future ozone levels. We quantify a comprehensive suite of ozone-related mortality and morbidity impacts including emergency department visits, hospital admissions, acute respiratory symptoms, and lost school days, and estimate the economic value of these impacts. Both GCMs project average daily maximum temperature to increase by 1–4°C and 1–5 ppb increases in daily 8-hr maximum ozone at 2030, though each climate scenario produces ozone levels that vary greatly over space and time. We estimate tens to thousands of additional ozone-related premature deaths and illnesses per year for these two scenarios and calculate an economic burden of these health outcomes of hundreds of millions to tens of billions of U.S. dollars (2010$).

Implications:?Near-term changes to the climate have the potential to greatly affect ground-level ozone. Using a 2030 emission inventory with regional climate fields downscaled from two general circulation models, we project mean temperature increases of 1 to 4°C and climate-driven mean daily 8-hr maximum ozone increases of 1–5 ppb, though each climate scenario produces ozone levels that vary significantly over space and time. These increased ozone levels are estimated to result in tens to thousands of ozone-related premature deaths and illnesses per year and an economic burden of hundreds of millions to tens of billions of U.S. dollars (2010$).     

Effects of copper fungicide residues on the microbial function of vineyard soils

The use of copper-based fungicides leads to an accumulation of copper (Cu) in vineyard soils, potentially causing adverse effects to the microbial function and fertility of the soil. This study used a soil microcosm approach to assess the effects of Cu accumulation on microbial function in vineyard soils. Surface soil samples were collected from 10 vineyards and a number of un-impacted reference sites in each of three different viticultural regions of Australia. The field-collected soils were transferred to microcosms and maintained for up to 93 days in the laboratory at 20–22 °C and 60 % of their maximum water-holding capacity. The microbial function of the soils was indicated by measuring phosphomonoesterase, arylsulfatase, urease, and phenol oxidase activities. In general, the vineyard soils had greater concentrations of Cu and lower enzyme activities than in the reference soils, although a weak negative relationship between Cu and enzyme activity could only be found for phosphomonoesterase activity. The results show that soil physical–chemical properties (i.e., organic carbon, pH) are greater determinants of soil enzyme activity than increased soil Cu concentration at the Cu concentrations present in vineyard soils.     

Ownership property size,landscape structure,and spatial relationships in the Edwards Plateau of Texas (USA): landscape scale habitat management implications

The present research focused on using spatial analysis to determine relationships among land ownership property sizes and landscape structure, with a focus on conservation management implications. Indices and metrics of ownership property sizes and landscape structure were calculated for 20 km buffer areas around 31 North American Breeding Bird Survey transects, 12 located within the Edwards Plateau ecoregion and 18 in contiguous ecoregions. The number of bird species observed at each transect provided a measure of avian species richness associated with land cover classes for each respective transect (González in Urban influence on diversity of avifauna in the Edwards Plateau of Texas: effect of property sizes on rural landscape structure, Texas A&M University, 2005). Spatial correlations were calculated between each pair of the landscape indices. Spatial analysis identified a “threshold of habitat fragmentation” for the 500 acre (ac) ownership property size. Significant spatial correlations among variables showed that property sizes lower than 500 ac produced habitat fragmentation represented by a decrease in mean patch size (MN) and proximity among habitat patches (Index PROX). Spatial analysis also made possible the prioritization of ecological sub-regions of the Edwards Plateau for conservation or restoration. The Live Oak-Mesquite Savannah showed the highest average ownership property size (7305 ac) and the highest values of patch richness. Based on the results, management in the Live Oak-Mesquite Savannah sub-region should focus on the conservation of land mosaic diversity to assure native avian species turnover (Whittaker 1972). In Balcones Canyon Lands, 64 % of land was covered by farms smaller than 500 ac and the overall average ownership property size was above the threshold of fragmentation (1440 ac), implying that management policies there should focus both on habitat conservation and on restoration. In contrast, 71 % of land in the Lampasas Cut Plains was covered by farms smaller than 500 ac, and average ownership property size was very close to the fragmentation threshold (625 ac). Consequently, the results indicate that management in the Lampasas Cut Plains sub-region should focus on habitat restoration (e.g., corridors that connect isolated habitat patches). In general, the threshold of ownership property size, 500 ac, is important for conservation planning because below that threshold of property size, habitat patch size begins to decrease and the distance between equivalent patches of habitat increases. Isolated patches act as islands within a sea of less suitable habitat which produce negative effects on biodiversity. Identifying the spatial characteristics indicative of habitat fragmentation, or the likelihood thereof, is an important issue for conservation planning in places with urban sprawl influence.     

Comparison of speciation sampler and PC-BOSS fine particulate matter organic material results obtained in Lindon, Utah, during winter 2001-2002

The Particle Concentrator-Brigham Young University Organic Sampling System (PC-BOSS) has been previously verified as being capable of measuring total fine particulate matter (PM2.5), including semi-volatile species. The present study was conducted to determine if the simple modification of a commercial speciation sampler with a charcoal denuder followed by a filter pack containing a quartz filter and a charcoal-impregnated glass (CIG) fiber filter would allow for the measurement of total PM2.5, including semi-volatile organic material. Data were collected using an R&P (Rupprecht and Pastasnik Co., Inc.) Partisol Model 2300 speciation sampler; an R&P Partisol speciation sampler modified with a BOSS denuder, followed by a filter pack with a quartz and a CIG filter; a Met One spiral aerosol speciation sampler (SASS); and the PC-BOSS from November 2001 to March 2002 at a U.S. Environmental Protection Agency (EPA) Science to Achieve Results (STAR) sampling site in Lindon, UT. Total PM2.5 mass, ammonium nitrate (both nonvolatile and semi-volatile), ammonium sulfate, organic carbon (both non-volatile and semi-volatile), and elemental carbon were determined on a 24-hr basis. Results obtained with the individual samplers were compared to determine the capability of the modified R&P speciation sampler for measuring total PM2.5, including semi-volatile components. Data obtained with the modified speciation sampler agreed with the PC-BOSS results. Data obtained with the two unmodified speciation samplers were low by an average of 26% because of the loss of semi-volatile organic material from the quartz filter during sample collection.