Genomic patterns in the widespread Eurasian lynx shaped by Late Quaternary climatic fluctuations and anthropogenic impacts.

Disentangling the contribution of long-term evolutionary processes and recent anthropogenic impacts to current genetic patterns of wildlife species is key for assessing genetic risks and designing conservation strategies. Here, we used 80 whole nuclear genomes and 96 mitogenomes from populations of the Eurasian lynx covering a range of conservation statuses, climatic zones and subspecies across Eurasia to infer the demographic history, reconstruct genetic patterns and discuss the influence of long-term isolation and/or more recent human-driven changes. Our results show that Eurasian lynx populations shared a common history until 100 kya, when Asian and European populations started to diverge and both entered a period of continuous and widespread decline, with western populations, except Kirov, maintaining lower effective sizes than eastern populations. Population declines and increased isolation in more recent times likely drove the genetic differentiation between geographically and ecologically close westernmost European populations. By contrast, and despite the wide range of habitats covered, populations are quite homogeneous genetically across the Asian range, showing a pattern of isolation by distance and providing little genetic support for the several proposed subspecies. Mitogenomic and nuclear divergences and population declines starting during the Late Pleistocene can be mostly attributed to climatic fluctuations and early human influence, but the widespread and sustained decline since the Holocene is more probably the consequence of anthropogenic impacts which intensified during the last centuries, especially in western Europe. Genetic erosion in isolated European populations and lack of evidence for long-term isolation argue for the restoration of lost population connectivity

Genomic Insights Into the Origin, Decline and Recovery of the Once Critically Endangered Iberian Lynx

The Iberian lynx was at the brink of extinction by the year 2000 but has since then, and thanks to intensive conservation measures, gone through a remarkable recovery, providing a much-welcomed and encouraging conservation success story. Genetic issues have probably contributed to the decline in the past, and the genetic management of inbreeding and genetic diversity is likely contributing to its recent recovery. The species was an early adopter of genetic and genomic approaches, and the combination of an extreme decline, an intensive monitoring and management programme and extensive genomic resources and data makes the Iberian lynx an excellent model for conservation genomics. Here, we review how genetic and genomic data have contributed to the knowledge of the species evolutionary and demographic history, the evaluation of the genetic status of the species through time, including historical and ancient data, and how this information has prompted and guided conservation actions. In the process, genomics provided valuable insights into the dynamics of functional variation in bottlenecked populations and the consequences of intraspecific and interspecific admixtures. In more applied terms, the species is subjected to an ambitious genetic monitoring and management programme, covering captive, remnant and reintroduced populations, which has succeeded in improving the genetic status of the species and thereby contributed to its recovery. Current genomic work aims at expanding these contributions with novel genomic resources and data while capitalising on extensive demographic and genealogical data provided by the ongoing non-invasive genetic monitoring programme

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

Background Genome-wide association studies (GWAS) in Parkinson's disease have increased the scope of biological knowledge about the disease over the past decade. We aimed to use the largest aggregate of GWAS data to identify novel risk loci and gain further insight into the causes of Parkinson's disease. Methods We did a meta-analysis of 17 datasets from Parkinson's disease GWAS available from European ancestry samples to nominate novel loci for disease risk. These datasets incorporated all available data. We then used these data to estimate heritable risk and develop predictive models of this heritability. We also used large gene expression and methylation resources to examine possible functional consequences as well as tissue, cell type, and biological pathway enrichments for the identified risk factors. Additionally, we examined shared genetic risk between Parkinson's disease and other phenotypes of interest via genetic correlations followed by Mendelian randomisation. Findings Between Oct 1, 2017, and Aug 9, 2018, we analysed 7·8 million single nucleotide polymorphisms in 37 688 cases, 18 618 UK Biobank proxy-cases (ie, individuals who do not have Parkinson's disease but have a first degree relative that does), and 1·4 million controls. We identified 90 independent genome-wide significant risk signals across 78 genomic regions, including 38 novel independent risk signals in 37 loci. These 90 variants explained 16–36% of the heritable risk of Parkinson's disease depending on prevalence. Integrating methylation and expression data within a Mendelian randomisation framework identified putatively associated genes at 70 risk signals underlying GWAS loci for follow-up functional studies. Tissue-specific expression enrichment analyses suggested Parkinson's disease loci were heavily brain-enriched, with specific neuronal cell types being implicated from single cell data. We found significant genetic correlations with brain volumes (false discovery rate-adjusted p=0·0035 for intracranial volume, p=0·024 for putamen volume), smoking status (p=0·024), and educational attainment (p=0·038). Mendelian randomisation between cognitive performance and Parkinson's disease risk showed a robust association (p=8·00 × 10−7). Interpretation These data provide the most comprehensive survey of genetic risk within Parkinson's disease to date, to the best of our knowledge, by revealing many additional Parkinson's disease risk loci, providing a biological context for these risk factors, and showing that a considerable genetic component of this disease remains unidentified. These associations derived from European ancestry datasets will need to be followed-up with more diverse data. Funding The National Institute on Aging at the National Institutes of Health (USA), The Michael J Fox Foundation, and The Parkinson's Foundation (see appendix for full list of funding sources)

Biomedical colonialism or local autonomy?: local healers in the fight against tuberculosis

Analiza el papel de los agentes médicos autóctonos y sus conocimientos en las campañas antituberculosas contemporáneas en el África subsahariana. Sitúa la medicina contemporánea, llevada a cabo en África en la herencia cultural de la medicina colonial, para comprender el marco histórico en el que se desarrollaron, a partir de los años setenta del siglo XX, las estrategias de la Organización Mundial de la Salud de promoción y desarrollo de las medicinas 'tradicionales'. En los proyectos sanitarios analizados, se evalúan las prácticas médicas locales y se entrenan a los agentes autóctonos para integrarlos en actividades estrictamente biomédicas: identificación de síntomas, remisión a hospitales o supervisión de tratamientos farmacológicos.The article explores the role played by indigenous medical agents, and their knowledge, within contemporary tuberculosis campaigns in sub-Saharan Africa. To understand the historical framework within which the World Health Organization devised its strategies to promote and develop traditional medicine as of the 1970s, the article contextualizes contemporary medicine as a cultural legacy of colonial medicine. Under the public healthcare projects analyzed in the article, local medical practices were assessed and indigenous agents trained so they could take part in strictly biomedical activities, like symptom identification, referrals to hospitals, or supervision of drug treatments.Trabajo realizado para la obtención del Diploma de Estudios Avanzados (DEA) en el programa de doctorado Salud: Antropología e Historia, bajo la dirección de la profesora Rosa María Medina Doménech

Electronic structure and properties of Cu2O

The structural and electronic properties of Cu2O have been investigated using the periodic Hartree-Fock method and a posteriori density-functional corrections. The lattice parameter, bulk modulus, and elastic constants have been calculated. The electronic structure of and bonding in Cu2O are analyzed and compared with x-ray photoelectron spectroscopy spectra, showing a good agreement for the valence-band states. To check the quality of the calculated electron density, static structure factors and Compton profiles have been calculated, showing a good agreement with the available experimental data. The effective electron and hole masses have been evaluated for Cu2O at the center of the Brillouin zone. The calculated interaction energy between the two interpenetrated frameworks in the cuprite structure is estimated to be around -6.0 kcal/mol per Cu2O formula. The bonding between the two independent frameworks has been analyzed using a bimolecular model and the results indicate an important role of d10-d10 type interactions between copper atoms

Intra-chromosomal estimates of inbreeding and coancestry in the Spanish Holstein cattle population

In recent years, inbreeding and coancestry are being estimated from genome-wide molecular information using a large number of SNPs. Molecular inbreeding and coancestry can be calculated for the whole genome or for particular regions of the genome. In this study, genome-based inbreeding and coancestry were estimated per chromosome and at intra-chromosomal level in a group of Holstein animals genotyped with the Illumina BovineSNP50 BeadChip. After applying filtering criteria, the genomic dataset included 36,693 autosomal SNPs and 10,569 animals. Genome-based inbreeding and coancestry at intra-chromosomal level were calculated using sliding windows of approximately 5 Mb. The results showed differential patterns of inbreeding and coancestry on specific chromosome regions. These patterns provide a more detailed picture of genetic diversity that could be used, for example, for the detection of regions with low levels of genetic diversity that require a specific genetic management in conservation programmes. (C) 2016 Elsevier B.V. All rights reserved

Why is grazing management being overlooked in climate adaptation policy?

In 2018, two studies were conducted by Canada’s Parliament on the connections between climate change and agriculture. Links between grazing management and climate change adaptation and mitigation are included in the testimonies gathered during these studies but the resulting final reports are silent on the topic. Analysis of 112 parliamentary files revealed insights on (1) the knowledge about grazing management that was omitted from the two final reports, (2) the social contexts that informed the processes of hearing testimonies and developing the reports, and (3) the underlying ideologies and normative assumptions reflected in these studies. Overall, the current state of policy regarding climate change and agriculture emphasizes technical, scientific, and expensive solutions, and as a result, the benefits of grazing management are overlooked. We argue transformations toward sustainable, climate adaptive agriculture require an ongoing examination of how political structures, knowledge hierarchies, and underlying ideologies inform and narrow policy outcomes