An Integrative Method for Accurate Comparative Genome Mapping

We present MAGIC, an integrative and accurate method for comparative genome mapping. Our method consists of two phases: preprocessing for identifying “maximal similar segments,” and mapping for clustering and classifying these segments. MAGIC's main novelty lies in its biologically intuitive clustering approach, which aims towards both calculating reorder-free segments and identifying orthologous segments. In the process, MAGIC efficiently handles ambiguities resulting from duplications that occurred before the speciation of the considered organisms from their most recent common ancestor. We demonstrate both MAGIC's robustness and scalability: the former is asserted with respect to its initial input and with respect to its parameters' values. The latter is asserted by applying MAGIC to distantly related organisms and to large genomes. We compare MAGIC to other comparative mapping methods and provide detailed analysis of the differences between them. Our improvements allow a comprehensive study of the diversity of genetic repertoires resulting from large-scale mutations, such as indels and duplications, including explicitly transposable and phagic elements. The strength of our method is demonstrated by detailed statistics computed for each type of these large-scale mutations. MAGIC enabled us to conduct a comprehensive analysis of the different forces shaping prokaryotic genomes from different clades, and to quantify the importance of novel gene content introduced by horizontal gene transfer relative to gene duplication in bacterial genome evolution. We use these results to investigate the breakpoint distribution in several prokaryotic genomes

Competition between normal and intruder states inside the "Island of Inversion"

The beta decay of the exotic 30Ne (N=20) is reported. For the first time, the low-energy level structure of the N=19, 30Na (Tz = 4), is obtained from beta-delayed gamma spectroscopy using fragment-beta-gamma-gamma coincidences. The level structure clearly displays "inversion", i.e., intruder states with mainly 2p2h configurations displacing the normal states to higher excitation energies. The good agreement in excitation energies and the weak and electromagnetic decay patterns with Monte Carlo Shell Model calculations with the SDPF-M interaction in the sdpf valence space illustrates the small d3/2 - f7/2 shell gap. The relative position of the "normal dominant" and "intruder dominant" excited states provides valuable information to understand better the N=20 shell gap.Comment: 4 pages, 5 figure

Predicting the impacts of chemical pollutants on animal groups

Wildlife are exposed to an increasing number and diversity of chemical pollutants.Chemical pollutants can elicit a range of sublethal effects on individual organisms, but research on how these contaminants affect social interactions and animal groups is severely lacking.It is imperative that perspectives from behavioural ecology and ecotoxicology are integrated, to increase our understanding of how contaminant effects on individuals might cascade to group-level processes.We present a conceptual framework for researchers and practitioners to guide the study of how chemical pollutants might affect the emergence, organisation, and function of animal social groups.Chemical pollution is among the fastest-growing agents of global change. Synthetic chemicals with diverse modes-of-action are being detected in the tissues of wildlife and pervade entire food webs. Although such pollutants can elicit a range of sublethal effects on individual organisms, research on how chemical pollutants affect animal groups is severely lacking. Here we synthesise research from two related, but largely segregated fields – ecotoxicology and behavioural ecology – to examine pathways by which chemical contaminants could disrupt processes that govern the emergence, self-organisation, and collective function of animal groups. Our review provides a roadmap for prioritising the study of chemical pollutants within the context of sociality and highlights important methodological advancements for future research