Utilisation des bioessais "in situ" (substrats artificiels) pour caractériser la qualité des eaux de rivière à l'aide du périphyton

La dynamique de croissance du périphyton sur des substrats artificiels immergés à l'amont et à l'aval de secteurs de cours d'eau recevant des rejets polluants a été utilisée pour évaluer le niveau de pollution. La méthode est basée sur la détermination de paramètres globaux (matières organiques, pigments chlorophylliens, respiration, photosynthèse, assimilation hétérotrophe) qui permettent de caractériser le développement des communautés photoautotrophes et hétérotrophes sur les substrats. Le taux de croissance et l'activité hétérotrophe de ces communautés évoluent au cours de la durée d'immersion des substrats selon un modèle général qui est décrit à partir de séries de données recueillies sur trois cours d'eau. Les résultats obtenus sur 22 stations montrent que ces paramètres constituent des indicateurs de pollution plus sensibles que ceux basés sur la composition spécifique des communautés de périphyton

Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results?

Next-generation sequencing technologies have opened a new era of research in population genetics. Following these new sequencing opportunities, the use of restriction enzyme-based genotyping techniques, such as restriction site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to SNP calling, the laboratory and bioinformatic parameters of enzyme-based techniques have been investigated in the literature. However, the impact of those parameters on downstream analyses and biological results remains less documented. In this study, we investigated the effects of sevral pre- and post-sequencing settings on ddRAD-seq results for two biological systems: a complex of butterfly species (Coenonympha sp.) and several populations of common beech (Fagus sylvatica). Our results suggest that pre-sequencing parameters (i.e., DNA quantity, number of PCR cycles during library preparation) have a significant impact on the number of recovered reads and SNPs, on the number of unique alleles and on individual heterozygosity. In the same way, we found that post-sequencing settings (i.e., clustering and minimum coverage thresholds) influenced loci reconstruction (e.g., number of loci, mean coverage) and SNP calling (e.g., number of SNPs; heterozygosity) but had only a marginal impact on downstream analyses (e.g., measure of genetic differentiation, estimation of individual admixture, and demographic inferences). In addition, replication analyses confirmed the reproducibility of the ddRAD-seq procedure. Overall, this study assesses the degree of sensitivity of ddRAD-seq data to pre- and post-sequencing protocols, and illustrates its robustness when studying population genetics