ngsLD: evaluating linkage disequilibrium using genotype likelihoods

MOTIVATION: Linkage disequilibrium measures the correlation between genetic loci and is highly informative for association mapping and population genetics. As many studies rely on called genotypes for estimating linkage disequilibrium, their results can be affected by data uncertainty, especially when employing a low read depth sequencing strategy. Furthermore, there is a manifest lack of tools for the analysis of large-scale, low-depth and short-read sequencing data from non-model organisms with limited sample sizes. RESULTS: ngsLD addresses these issues by estimating linkage disequilibrium directly from genotype likelihoods in a fast, reliable and user-friendly implementation. This method makes use of the full information available from sequencing data and provides accurate estimates of linkage disequilibrium patterns compared to approaches based on genotype calling. We conducted a case study to investigate how linkage disequilibrium decays over physical distance in two avian species. AVAILABILITY: The methods presented in this work were implemented in C/C and are freely available for non-commercial use from https://github.com/fgvieira/ngsLD

No longer locally extinct? Tracing the origins of a lion (Panthera leo) living in Gabon

Lions (Panthera leo) are of particular conservation concern due to evidence of recent, widespread population declines in what has hitherto been seen as a common species, robust to anthropogenic disturbance. Here we use non-invasive methods to recover complete mitochondrial genomes from single hair samples collected in the field in order to explore the identity of the Gabonese Plateaux Batéké lion. Comparison of the mitogenomes against a comprehensive dataset of African lion sequences that includes relevant geographically proximate lion populations from both contemporary and ancient sources, enabled us to identify the Plateaux Batéké lion as a close maternal relative to now extirpated populations found in Gabon and nearby Congo during the twentieth century, and to extant populations of Southern Africa. Our study demonstrates the relevance of ancient DNA methods to field conservation work, and the ability of trace field samples to provide copious genetic information about free-ranging animals.Acknowledgements We thank the laboratory technicians of the Centre for GeoGenetics and the staff of the Danish National High-Throughput DNA Sequencing Centre for technical assistance. This project received funding from the European Union�s Seventh Framework Programme for research, technological development and demonstration under grant agreement no. FP7-PEOPLE-2011-IEF-298820, and ERC Consolidator Grant 681396 � Extinction Genomics. Fieldwork in Gabon was funded by Panthera and The Aspinall Foundation. We thank the Staff at Projet Protection Gorilles Gabon and the Gabonese National Park Agency for their assistance in fieldwork. Thanks also to Tony King for helpful comments on the manuscript. Permission to collect and export the samples was granted by the respective Ministries of the Environment (Eaux et Forets) in Gabon and Congo, and by Gabon�s National Park Agency (ANPN).Scopu

Anisotropy of Upper Critical Field near Tc and Magnetic Gap of Superconducting URu2Si2 Single Crystal.

Studying thermal conductivity and STM spectra in the normal and magnetic phase of superconducting URu2Si2 single crystal, we found, that the magnetic gap, partially opened on the Fermi surface below Neel temperature TN = 17.5 K, is strongly anisotropic: gapped states mainly correspond to tetragonal ab plane

Evaluation of HBV-Like circulation in wild and farm animals from Brazil and Uruguay

The origin of the hepatitis B virus is a subject of wide deliberation among researchers. As a result, increasing academic interest has focused on the spread of the virus in different animal species. However, the sources of viral infection for many of these animals are unknown since transmission may occur from animal to animal, human to human, animal to human, and human to animal. The aim of this study was to evaluate hepadnavirus circulation in wild and farm animals (including animals raised under wild or free conditions) from different sites in Brazil and Uruguay using serological and molecular tools. A total of 487 domestic wild and farm animals were screened for hepatitis B virus (HBV) serological markers and tested via quantitative and qualitative polymerase chain reaction (PCR) to detect viral DNA. We report evidence of HBsAg (surface antigen of HBV) and total anti-HBc (HBV core antigen) markers as well as low-copy hepadnavirus DNA among domestic and wild animals. According to our results, which were confirmed by partial genome sequencing, as the proximity between humans and animals increases, the potential for pathogen dispersal also increases. A wider knowledge and understanding of reverse zoonoses should be sought for an effective One Health response