High performance computation of landscape genomic models including local indicators of spatial association

With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics – that is the combination of landscape ecology with population genomics – include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental data sets. samβada identifies candidate loci using genotype–environment associations while also incorporating multivariate analyses to assess the effect of many environmental predictor variables. This enables the inclusion of explanatory variables representing population structure into the models to lower the occurrences of spurious genotype–environment associations. In addition, samβada calculates local indicators of spatial association for candidate loci to provide information on whether similar genotypes tend to cluster in space, which constitutes a useful indication of the possible kinship between individuals. To test the usefulness of this approach, we carried out a simulation study and analysed a data set from Ugandan cattle to detect signatures of local adaptation with samβada, bayenv, lfmm and an FST outlier method (FDIST approach in arlequin) and compare their results. samβada – an open source software for Windows, Linux and Mac OS X available at http://lasig.epfl.ch/sambada – outperforms other approaches and better suits whole-genome sequence data processing

Harmonized biosafety regulations are key to trust building in regional agbiotech partnerships: the case of the Bt cotton project in East Africa

<p>Abstract</p> <p>Background</p> <p>The <it>Bacillus thuringiensis</it> (Bt) cotton public-private partnership (PPP) project in East Africa was designed to gather baseline data on the effect of Bt cotton on biodiversity and the possibility of gene flow to wild cotton varieties. The results of the project are intended to be useful for Kenya, Uganda, and Tanzania when applying for biosafety approvals. Using the backdrop of the different biosafety regulations in the three countries, we investigate the role of trust in the Bt cotton partnership in East Africa.</p> <p>Methods</p> <p>Data were collected by reviewing relevant project documents and peer-reviewed articles on Bt cotton in Tanzania, Kenya and Uganda; conducting face-to-face interviews with key informants of the project; and conducting direct observations of the project. Data were analyzed based on recurring and emergent themes to create a comprehensive narrative on how trust is understood and built among the partners and with the community.</p> <p>Results</p> <p>We identified three factors that posed challenges to building trust in the Bt cotton project in East Africa: different regulatory regimes among the three countries; structural and management differences among the three partner institutions; and poor public awareness of GM crops and negative perceptions of the private sector. The structural and management differences were said to be addressed through joint planning, harmonization of research protocols, and management practices, while poor public awareness of GM crops and negative perceptions of the private sector were said to be addressed through open communication, sharing of resources, direct stakeholder engagement and awareness creation. The regulatory differences remained outside the scope of the project.</p> <p>Conclusions</p> <p>To improve the effectiveness of agbiotech PPPs, there is first a need for a regulatory regime that is acceptable to both the public and private sector partners. Second, early and continuous joint planning; sharing of information; and transparency encourages accountability and fosters trust building. Third, direct stakeholder engagement and awareness creation builds trust between project partners and the community. A concern raised by the interviewees was the absence of a regulatory framework in Tanzania, which deterred active private sector participation in the project.</p

Drivers and risk factors for circulating African swine fever virus in Uganda, 2012–2013

We explored observed risk factors and drivers of infection possibly associated with African swine fever (ASF) epidemiology in Uganda. Representative sub-populations of pig farms and statistics were used in a case-control model. Indiscriminate disposal of pig viscera and waste materials after slaughter, including on open refuse dumps, farm-gate buyers collecting pigs and pig products from within a farm, and retention of survivor pigs were plausible risk factors. Wire mesh-protected windows in pig houses were found to be protective against ASF infection. Sighting engorged ticks on pigs, the presence of a lock for each pig pen and/or a gate at the farm entrance were significantly associated with infection/noninfection; possible explanations were offered. Strict adherence to planned within-farm and communitybased biosecurity, and avoidance of identified risk factors is recommended to reduce infection. Training for small-scale and emerging farmers should involve multidimensional and multidisciplinary approaches to reduce human-related risky behaviours driving infection.National Agricultural Research Organization (NARO) (4760UG) and the Department of Production Animal Studies and the Faculty of Veterinary Science, Onderstepoort, Pretoria, South Africa.http://www.elsevier.com/locate/rvsc2015-10-31hb201