Non-stationary patterns of isolation-by-distance: inferring measures of local genetic differentiation with Bayesian kriging

Patterns of isolation-by-distance arise when population differentiation increases with increasing geographic distances. Patterns of isolation-by-distance are usually caused by local spatial dispersal, which explains why differences of allele frequencies between populations accumulate with distance. However, spatial variations of demographic parameters such as migration rate or population density can generate non-stationary patterns of isolation-by-distance where the rate at which genetic differentiation accumulates varies across space. To characterize non-stationary patterns of isolation-by-distance, we infer local genetic differentiation based on Bayesian kriging. Local genetic differentiation for a sampled population is defined as the average genetic differentiation between the sampled population and fictive neighboring populations. To avoid defining populations in advance, the method can also be applied at the scale of individuals making it relevant for landscape genetics. Inference of local genetic differentiation relies on a matrix of pairwise similarity or dissimilarity between populations or individuals such as matrices of FST between pairs of populations. Simulation studies show that maps of local genetic differentiation can reveal barriers to gene flow but also other patterns such as continuous variations of gene flow across habitat. The potential of the method is illustrated with 2 data sets: genome-wide SNP data for human Swedish populations and AFLP markers for alpine plant species. The software LocalDiff implementing the method is available at http://membres-timc.imag.fr/Michael.Blum/LocalDiff.htmlComment: In press, Evolution 201

Wave-like spread of Ebola Zaire

In the past decade the Zaire strain of Ebola virus (ZEBOV) has emerged repeatedly into human populations in central Africa and caused massive die-offs of gorillas and chimpanzees. We tested the view that emergence events are independent and caused by ZEBOV variants that have been long resident at each locality. Phylogenetic analyses place the earliest known outbreak at Yambuku, Democratic Republic of Congo, very near to the root of the ZEBOV tree, suggesting that viruses causing all other known outbreaks evolved from a Yambuku-like virus after 1976. The tendency for earlier outbreaks to be directly ancestral to later outbreaks suggests that outbreaks are epidemiologically linked and may have occurred at the front of an advancing wave. While the ladder-like phylogenetic structure could also bear the signature of positive selection, our statistical power is too weak to reach a conclusion in this regard. Distances among outbreaks indicate a spread rate of about 50 km per year that remains consistent across spatial scales. Viral evolution is clocklike, and sequences show a high level of small-scale spatial structure. Genetic similarity decays with distance at roughly the same rate at all spatial scales. Our analyses suggest that ZEBOV has recently spread across the region rather than being long persistent at each outbreak locality. Controlling the impact of Ebola on wild apes and human populations may be more feasible than previously recognized

Improved detection of abrupt change in vegetation reveals dominant fractional woody cover decline in Eastern Africa

While cropland expansion and demand for woodfuel exert increasing pressure on woody vegetation in East Africa, climate change is inducing woody cover gain. It is however unclear if these contrasting patterns have led to net fractional woody cover loss or gain. Here we used non-parametric fractional woody cover (WC) predictions and breakpoint detection algorithms driven by satellite observations (Landsat and MODIS) and airborne laser scanning to unveil the net fractional WC change during 2001-2019 over Ethiopia and Kenya. Our results show that total WC loss was 4-times higher than total gain, leading to net loss. The contribution of abrupt WC loss (59%) was higher than gradual losses (41%). We estimated an annual WC loss rate of up to 5% locally, with cropland expansion contributing to 57% of the total loss in the region. Major hotspots of WC loss and degradation corridors were identified inside as well as surrounding protected areas, in agricultural lands located close to agropastoral and pastoral livelihood zones, and near highly populated areas. As the dominant vegetation type in the region, Acacia-Commiphora bushlands and thickets ecosystem was the most threatened, accounting 69% of the total WC loss, followed by montane forest (12%). Although highly outweighed by loss, relatively more gain was observed in woody savanna than in other ecosystems. These results reveal the marked impact of human activities on woody vegetation and highlight the importance of protecting endangered ecosystems from increased human activities for mitigating impacts on climate and supporting sustainable ecosystem service provision in East Africa.Peer reviewe

Characterization of the frequency of extreme events by the Generalized Pareto Distribution

Based on recent results in extreme value theory, we use a new technique for the statistical estimation of distribution tails. Specifically, we use the Gnedenko-Pickands-Balkema-de Haan theorem, which gives a natural limit law for peak-over-threshold values in the form of the Generalized Pareto Distribution (GPD). Useful in finance, insurance, hydrology, we investigate here the earthquake energy distribution described by the Gutenberg-Richter seismic moment-frequency law and analyze shallow earthquakes (depth h < 70 km) in the Harvard catalog over the period 1977-2000 in 18 seismic zones. The whole GPD is found to approximate the tails of the seismic moment distributions quite well above moment-magnitudes larger than mW=5.3 and no statistically significant regional difference is found for subduction and transform seismic zones. We confirm that the b-value is very different in mid-ocean ridges compared to other zones (b=1.50=B10.09 versus b=1.00=B10.05 corresponding to a power law exponent close to 1 versus 2/3) with a very high statistical confidence. We propose a physical mechanism for this, contrasting slow healing ruptures in mid-ocean ridges with fast healing ruptures in other zones. Deviations from the GPD at the very end of the tail are detected in the sample containing earthquakes from all major subduction zones (sample size of 4985 events). We propose a new statistical test of significance of such deviations based on the bootstrap method. The number of events deviating from the tails of GPD in the studied data sets (15-20 at most) is not sufficient for determining the functional form of those deviations. Thus, it is practically impossible to give preference to one of the previously suggested parametric families describing the ends of tails of seismic moment distributions.Comment: pdf document of 21 pages + 2 tables + 20 figures (ps format) + one file giving the regionalizatio

Analyzing Vegetation Trends with Sensor Data from Earth Observation Satellites

Abstract This thesis aims to advance the analysis of nonlinear trends in time series of vegetation data from Earth observation satellite sensors. This is accomplished by developing fast, efficient methods suitable for large volumes of data. A set of methods, tools, and a framework are developed and verified using data from regions containing vegetation change hotspots. First, a polynomial-fitting scheme is tested and applied to annual Global Inventory Modeling and Mapping Studies (GIMMS)–Normalized Difference Vegetation Index (NDVI) observations for North Africa for the period 1982–2006. Changes in annual observations are divided between linear and nonlinear (cubic, quadratic, and concealed) trend behaviors. A concealed trend is a nonlinear change which does not result in a net change in the amount of vegetation over the period. Second, a systematic comparison between parametric and non-parametric techniques for analyzing trends in annual GIMMS-NDVI data is performed at fifteen sites (located in Africa, Spain, Italy, and Iraq) to compare how trend type and departure from normality assumptions affect each method’s accuracy in detecting long-term change. Third, a user-friendly program (Detecting Breakpoints and Estimating Segments in Trend, DBEST) has been developed which generalizes vegetation trends to main features, and characterizes vegetation trend changes. The outputs of DBEST are the simplified trend, the change type (abrupt or non-abrupt), and estimates for the characteristics (time and magnitude) of the change. DBEST is tested and evaluated using both simulated NDVI data, and actual NDVI time series for Iraq for the period 1982-2006. Finally, a decision-making framework is presented to help analysts perform comprehensive analyses of trend/change in time series of satellite sensor data. The framework is based on a conceptual model of the main aspects of trend analyses, including identification of the research question, the required data, the appropriate variables, and selection of efficient analysis methods. To verify the framework, it is applied to four case studies (located in Burkina Faso, Spain, Sweden, and Senegal) using Moderate-resolution Imaging Spectroradiometer (MODIS)–NDVI data for the period 2000–2013. Each of the case studies successfully achieved its research aim(s), showing that the framework can achieve the main goal of the study which is to advance the analysis of nonlinear changes in vegetation. The methods developed in this thesis can help to contribute more accurate information about vegetation dynamics to the field of land cover change research