Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.     

Sample size calculations for Bayesian prediction of bovine viral-diarrhoea-virus infection in beef herds

We used a Bayesian classification approach to predict the bovine viral-diarrhoea-virus infection status of a herd when the prevalence of persistently infected animals in such herds is very small (e.g. <1%). An example of the approach is presented using data on beef herds in Wyoming, USA. The approach uses past covariate information (serum-neutralization titres collected on animals in 16 herds) within a predictive model for classification of a future observable herd. Simulations to estimate misclassification probabilities for different misclassification costs and prevalences of infected herds can be used as a guide to the sample size needed for classification of a future herd.     

Assessing Impacts of Crested Wheatgrass AND Native Species Establishment on Soil Characteristics in Reclaimed LAND Using Bayesian Posterior Predictive Distributions

We examined the interacting effects of drastic disturbance and re‐vegetation communities on the development of soil properties over time. We compared soil characteristics from an undisturbed reference site with reclaimed mine sites that differed by vegetation type and time since reclamation: Three sites were seeded solely with crested wheatgrass (Agropyron cristatum) (11, 16, and 29 years old), and two were seeded with native cool‐season grass mixes (14 and 26 years old). We sampled soil at two depths (0–5 and 5–15 cm) for soil macroaggregate and microaggregate weights, aggregate carbon to nitrogen (C : N) ratios, and microbial abundance. We employed a Bayesian bivariate model to account for potential correlations in soil properties across depths and compared soil properties across sites using posterior predictive distributions. We found that all reclaimed soils, regardless of vegetation type, had total aggregate weights that were similar to the undisturbed reference soil but had a larger proportion of macroaggregates than the reference soil. Aggregate C : N ratios were similar between the undisturbed reference and crested wheatgrass soils, while the reclaimed native cool‐season grass soils had lower C : N ratios in the top 5 cm. Total microbial abundance in soils seeded with crested wheatgrass was an order of magnitude lower than that in soils occupied by native species (both reclaimed and undisturbed). The presence of crested wheatgrass on the reclaimed sites alone did not differentiate all soil properties across our reclamation sites, but seeding this single, aggressive species may have contributed to maintaining different belowground characteristics on reclaimed soils. Copyright © 2015 John Wiley & Sons, Ltd.