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

Automatic fault mapping in remote optical images and topographic data with deep learning

International audienceFaults form dense, complex multi‐scale networks generally featuring a master fault and myriads of smaller‐scale faults and fractures off its trace, often referred to as damage. Quantification of the architecture of these complex networks is critical to understanding fault and earthquake mechanics. Commonly, faults are mapped manually in the field or from optical images and topographic data through the recognition of the specific curvilinear traces they form at the ground surface. However, manual mapping is time‐consuming, which limits our capacity to produce complete representations and measurements of the fault networks. To overcome this problem, we have adopted a machine learning approach, namely a U‐Net Convolutional Neural Network, to automate the identification and mapping of fractures and faults in optical images and topographic data. Intentionally, we trained the CNN with a moderate amount of manually created fracture and fault maps of low resolution and basic quality, extracted from one type of optical images (standard camera photographs of the ground surface). Based on a number of performance tests, we select the best performing model, MRef, and demonstrate its capacity to predict fractures and faults accurately in image data of various types and resolutions (ground photographs, drone and satellite images and topographic data). MRef exhibits good generalization capacities, making it a viable tool for fast and accurate mapping of fracture and fault networks in image and topographic data. The MRef model can thus be used to analyze fault organization, geometry, and statistics at various scales, key information to understand fault and earthquake mechanics