Testing Differences Between Pathogen Compositions with Small Samples and Sparse Data.

The structure of pathogen populations is an important driver of epidemics affecting crops and natural plant communities. Comparing the composition of two pathogen populations consisting of assemblages of genotypes or phenotypes is a crucial, recurrent question encountered in many studies in plant disease epidemiology. Determining whether there is a significant difference between two sets of proportions is also a generic question for numerous biological fields. When samples are small and data are sparse, it is not straightforward to provide an accurate answer to this simple question because routine statistical tests may not be exactly calibrated. To tackle this issue, we built a computationally intensive testing procedure, the generalized Monte Carlo plug-in test with calibration test, which is implemented in an R package available at https://doi.org/10.5281/zenodo.635791 . A simulation study was carried out to assess the performance of the proposed methodology and to make a comparison with standard statistical tests. This study allows us to give advice on how to apply the proposed method, depending on the sample sizes. The proposed methodology was then applied to real datasets and the results of the analyses were discussed from an epidemiological perspective. The applications to real data sets deal with three topics in plant pathology: the reproduction of Magnaporthe oryzae, the spatial structure of Pseudomonas syringae, and the temporal recurrence of Puccinia triticina.

IR laser extraction technique applied to oxygen isotope analysis of small biogenic silica samples.

An IR-laser fluorination technique is reported here for analyzing the oxygen isotope composition (delta18O) of microscopic biogenic silica grains (phytoliths and diatoms). Performed after a controlled isotopic exchanged (CIE) procedure, the laser fluorination technique that allows one to visually check the success of the fluorination reaction is faster than the conventional fluorination technique and allows analyzing delta18O of small to minute samples (1.6-0.3 mg) as required for high-resolution paleoenvironmental reconstructions. The long-term reproducibility achieved with the IR laser-heating fluorination/O2 delta18O analysis is lower than or equal to +/-0.26 per thousand (1 SD; n = 99) for phytoliths and +/-0.17 per thousand (1 SD; n = 47) for diatoms. When several CIE are taken into account in the SD calculation, the resulting reproducibility is lower than or equal to +/-0.51 per thousand for phytoliths (1 SD; n = 99; CIE > 5) and +/-0.54 per thousand (1 SD; n = 47; CIE = 13) for diatoms. A minimum reproducibility of +/-0.5 per thousand leads to an estimated uncertainty on delta18Osilica close to +/-0.5 per thousand. Resulting uncertainties on reconstructed temperature and delta18Oforming water are, respectively, +/-2 degrees C and +/-0.5 per thousand and fit in the precisions required for intertropical paleoenvironmental reconstructions. Several methodological points such as optimal extraction protocols and the necessity or not of performing two CIE prior to oxygen extraction are assessed.