Drivers of global variation in land ownership

Land ownership shapes natural resource management and social–ecological resilience, but the factors determining ownership norms in human societies remain unclear. Here we conduct a global empirical test of long‐standing theories from ecology, economics and anthropology regarding potential drivers of land ownership and territoriality. Prior theory suggests that resource defensibility, subsistence strategies, population pressure, political complexity and cultural transmission mechanisms may all influence land ownership. We applied multi‐model inference procedures based on logistic regression to cultural and environmental data from 102 societies, 71 with some form of land ownership and 31 with no land ownership. We found an increased probability of land ownership in mountainous environments, where patchy resources may be more cost effective to defend via ownership. We also uncovered support for the role of population pressure, with a greater probability of land ownership in societies living at higher population densities. Our results also show more land ownership when neighboring societies also practiced ownership. We found less support for variables associated with subsistence strategies and political complexity.     

Dengue virus activates polyreactive, natural IgG B cells after primary and secondary infection

Background

Dengue virus is transmitted by mosquitoes and has four serotypes. Cross-protection to other serotypes lasting for a few months is observed following infection with one serotype. There is evidence that low-affinity T and/or B cells from primary infections contribute to the severe syndromes often associated with secondary dengue infections. such pronounced immune-mediated enhancement suggests a dengue-specific pattern of immune cell activation. This study investigates the acute and early convalescent B cell response leading to the generation of cross-reactive and neutralizing antibodies following dengue infection.

Methodology/Principal Findings

We assayed blood samples taken from dengue patients with primary or secondary infection during acute disease and convalescence and compared them to samples from patients presenting with non-dengue related fever. Dengue induced massive early plasmablast formation, which correlated with the appearance of polyclonal, cross-reactive IgG for both primary and secondary infection. Surprisingly, the contribution of IgG to the neutralizing titer 4–7 days after fever onset was more than 50% even after primary infection.

Conclusions/Significance

Poly-reactive and virus serotype cross-reactive IgG are an important component of the innate response in humans during both primary and secondary dengue infection, and “innate specificities” seem to constitute part of the adaptive response in dengue. While of potential importance for protection during secondary infection, cross-reactive B cells will also compete with highly neutralizing B cells and possibly interfere with their development.     

Pathogen quantitation in complex matrices: a multi-operator comparison of DNA extraction methods with a novel assessment of PCR inhibition

Background

Mycobacterium bovis is the aetiological agent of bovine tuberculosis (bTB), an important recrudescent zoonosis, significantly increasing in British herds in recent years. Wildlife reservoirs have been identified for this disease but the mode of transmission to cattle remains unclear. There is evidence that viable M. bovis cells can survive in soil and faeces for over a year.

Methodology/Principal Findings

We report a multi-operator blinded trial for a rigorous comparison of five DNA extraction methods from a variety of soil and faecal samples to assess recovery of M. bovis via real-time PCR detection. The methods included four commercial kits: the QIAamp Stool Mini kit with a pre-treatment step, the FastDNA® Spin kit, the UltraClean™ and PowerSoil™ soil kits and a published manual method based on phenol:chloroform purification, termed Griffiths. M. bovis BCG Pasteur spiked samples were extracted by four operators and evaluated using a specific real-time PCR assay. A novel inhibition control assay was used alongside spectrophotometric ratios to monitor the level of inhibitory compounds affecting PCR, DNA yield, and purity. There were statistically significant differences in M. bovis detection between methods of extraction and types of environmental samples; no significant differences were observed between operators. Processing times and costs were also evaluated. To improve M. bovis detection further, the two best performing methods, FastDNA® Spin kit and Griffiths, were optimised and the ABI TaqMan environmental PCR Master mix was adopted, leading to improved sensitivities.

Conclusions

M. bovis was successfully detected in all environmental samples; DNA extraction using FastDNA® Spin kit was the most sensitive method with highest recoveries from all soil types tested. For troublesome faecal samples, we have used and recommend an improved assay based on a reduced volume, resulting in detection limits of 4.25×10⁵ cells g⁻¹ using Griffiths and 4.25×10⁶ cells g⁻¹ using FastDNA® Spin kit.     

Observations on the ultrastructure of the flagella and periplast in the Cryptophyceae

The flagella in Cryptomonas ovata Ehrenberg and two other un-named strains of Cryptomonas both bear stiff hairs with fine distal filaments of the same type as those found in the Xanthophyceae, the Chrysophyceae sensu stricto, the Phaeophyceae, the Bacillariophyceae, the Eustigmatophyceae and the Oomycetes. On the longer of the two flagella the hairs are 2·5 µm long and in two opposite rows whereas on the shorter flagellum they measure only 1 µm, are arranged in a single row and are more closely spaced. The long flagellum also bears a characteristic lateral swelling with a tuft of hairs of the same type as on the remainder of the flagellum, at approximately the level at which it emerges from the gullet. The hairs on the flagella of Hemiselmis rufescens Parke are distributed in a similar manner to those in Cryptomonas but they are more flexible and the swelling and tuft of hairs appear to be absent from the long flagellum. Hairs are apparently absent from the short flagellum of Chroomonas sp. The periplast in Cryptomonas ovata shows a hexagonal pattern in surface view and in sections of all three Cryptomonas strains appears as a typical plasmalemma underlain by a discontinuous layer of electron-dense material with variable substructure. The distribution of flagellar hairs and the structure of the periplast appear to be characters unique to the Cryptophyceae and these features emphasise the isolated position of this class of algae.     

Statistical models for monitoring and predicting effects of climate change and invasion on the free-living insects and a spider from sub-Antarctic Heard Island

Terrestrial ecosystems of sub-Antarctic islands are particularly sensitive to global and local human impacts, including climate change and species invasion. Invertebrates form a central component of these ecosystems. We conducted a stratified survey of 60 sites on sub-Antarctic Heard Island and used Poisson regression models to describe the spatial distribution and abundance of five of the ten free-living species captured. Acari and Collembola were not considered. Five species were not caught in traps in sufficient numbers to model. The distributions of species were described by altitude, vegetation type and aspect. The resulting distribution models can be used to both monitor and predict the effects of climate change and species invasion on this unique and valuable ecosystem.     

A global approach to resistance monitoring

Transgenic crops producing insecticidal toxins from the bacterium Bacillus thuringiensis (Bt) have been grown in many parts of the world since 1996. In the United States, the Environmental Protection Agency (EPA) has required that industry submit insect resistance management (IRM) plans for each Bt corn and cotton product commercialized. A coalition of stakeholders including the EPA, USDA, academic scientists, industry, and grower organizations have cooperated in developing specific IRM strategies. Resistance monitoring (requiring submission of annual reports to the EPA), and a remedial action plan addressing any contingency if resistance should occur, are important elements of these strategies. At a global level, Monsanto conducts baseline susceptibility studies (prior to commercialization), followed by monitoring studies on target pest populations, for all of its commercialized Bt crop products. To date, Monsanto has conducted baseline/monitoring studies in Argentina, Australia, Brazil, Canada, China, Colombia, India, Mexico, the Philippines, South Africa, Spain, and the United States. Examples of pests on which resistance monitoring has been conducted include cotton bollworm, Helicoverpa zea, European corn borer, Ostrinia nubilalis, pink bollworm, Pectinophora gossypiella, Southwestern corn borer, Diatraea grandiosella, tobacco budworm, Heliothis virescens, and western corn rootworm, Diabrotica virgifera virgifera, in the United States, cotton bollworm, Helicoverpa armigera, in China, India and Australia, and H. virescens and H. zea in Mexico. No field-selected resistance to Bt crops has been documented.     

cnvCapSeq: detecting copy number variation in long-range targeted resequencing data

Targeted resequencing technologies have allowed for efficient and cost-effective detection of genomic variants in specific regions of interest. Although capture sequencing has been primarily used for investigating single nucleotide variants and indels, it has the potential to elucidate a broader spectrum of genetic variation, including copy number variants (CNVs). Various methods exist for detecting CNV in whole-genome and exome sequencing datasets. However, no algorithms have been specifically designed for contiguous target sequencing, despite its increasing importance in clinical and research applications. We have developed cnvCapSeq, a novel method for accurate and sensitive CNV discovery and genotyping in long-range targeted resequencing. cnvCapSeq was benchmarked using a simulated contiguous capture sequencing dataset comprising 21 genomic loci of various lengths. cnvCapSeq was shown to outperform the best existing exome CNV method by a wide margin both in terms of sensitivity (92.0 versus 48.3%) and specificity (99.8 versus 70.5%). We also applied cnvCapSeq to a real capture sequencing cohort comprising a contiguous 358 kb region that contains the Complement Factor H gene cluster. In this dataset, cnvCapSeq identified 41 samples with CNV, including two with duplications, with a genotyping accuracy of 99%, as ascertained by quantitative real-time PCR.     

The roles of demography and genetics in the early stages of colonization

Colonization success increases with the size of the founding group. Both demographic and genetic factors underlie this relationship, yet because genetic diversity normally increases with numbers of individuals, their relative importance remains unclear. Furthermore, their influence may depend on the environment and may change as colonization progresses from establishment through population growth and then dispersal. We tested the roles of genetics, demography and environment in the founding of Tribolium castaneum populations. Using three genetic backgrounds (inbred to outbred), we released individuals of four founding sizes (2–32) into two environments (natal and novel), and measured establishment success, initial population growth and dispersal. Establishment increased with founding size, whereas population growth was shaped by founding size, genetic background and environment. Population growth was depressed by inbreeding at small founding sizes, but growth rates were similar across genetic backgrounds at large founding size, an interaction indicating that the magnitude of the genetic effects depends upon founding population size. Dispersal rates increased with genetic diversity. These results suggest that numbers of individuals may drive initial establishment, but that subsequent population growth and spread, even in the first generation of colonization, can be driven by genetic processes, including both reduced growth owing to inbreeding depression, and increased dispersal with increased genetic diversity.