BackgroundLocal adaptation to divergent environmental conditions can promote population genetic differentiation even in the absence of geographic barriers and hence, lead to speciation. Perturbations by catastrophic events, however, can distort such parapatric ecological speciation processes. Here, we asked whether an exceptionally strong flood led to homogenization of gene pools among locally adapted populations of the Atlantic molly (Poecilia mexicana, Poeciliidae) in the Cueva del Azufre system in southern Mexico, where two strong environmental selection factors (darkness within caves and/or presence of toxic H2S in sulfidic springs) drive the diversification of P. mexicana. Nine nuclear microsatellites as well as heritable female life history traits (both as a proxy for quantitative genetics and for trait divergence) were used as markers to compare genetic differentiation, genetic diversity, and especially population mixing (immigration and emigration) before and after the flood.ResultsHabitat type (i.e., non-sulfidic surface, sulfidic surface, or sulfidic cave), but not geographic distance was the major predictor of genetic differentiation. Before and after the flood, each habitat type harbored a genetically distinct population. Only a weak signal of individual dislocation among ecologically divergent habitat types was uncovered (with the exception of slightly increased dislocation from the Cueva del Azufre into the sulfidic creek, El Azufre). By contrast, several lines of evidence are indicative of increased flood-induced dislocation within the same habitat type, e.g., between different cave chambers of the Cueva del Azufre.ConclusionsThe virtual absence of individual dislocation among ecologically different habitat types indicates strong natural selection against migrants. Thus, our current study exemplifies that ecological speciation in this and other systems, in which extreme environmental factors drive speciation, may be little affected by temporary perturbations, as adaptations to physico-chemical stressors may directly affect the survival probability in divergent habitat types.

Despite considerable progress in the production of alternative diets, small concentrations of antinutrients remain common in aquaculture nutrition, resulting in a perpetual limitation with regard to the inclusion of plant ingredients in aquafeeds. These compounds are known to impair the general performance of fish when fed for a prolonged period of time, potentially affecting the animal's susceptibility to stress, too. Therefore, a 12-week feeding trial was conducted to examine the chronic effects of purified rapeseed protein concentrate (RPC), containing low concentrations of glucosinolates and phytic acid, on the relative expression of multiple target genes in the liver of juvenile turbot (Psetta maxima, L.). Our results revealed divergent patterns of gene expression, suggesting different coping strategies dependent on the grade of RPC substitution. Data implies increased metabolic rate of turbot fed a 33% RPC-substituted diet due to an upregulation of cytochrome c oxidase mRNA, accompanied by minor adjustments in metabolic pathways. While no signs of reduced welfare were found, data adumbrate a beneficial hormetic reaction. In the highest treatment level (66% RPC), diminished fish condition and reduced growth performance coincided with a downregulation of insulin-like growth factor I, further indicating a potential impaired resistance to stress. An additional downregulation of transferrin hints towards an increased liability to bacterial infections.

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Detection of genetic variants in clinically relevant genomic hot-spot regions has become a promising application of next-generation sequencing technology in precision oncology. Effective personalized diagnostics requires the detection of variants with often very low frequencies. This can be achieved by targeted, short-read sequencing that provides high sequencing depths. However, rare genetic variants can contain crucial information for early cancer detection and subsequent treatment success, an inevitable level of background noise usually limits the accuracy of low frequency variant calling assays. To address this challenge, we developed DEEPGENTM, a variant calling assay intended for the detection of low frequency variants within liquid biopsy samples. We processed reference samples with validated mutations of known frequencies (0%–0.5%) to determine DEEPGENTM’s performance and minimal input requirements. Our findings confirm DEEPGENTM’s effectiveness in discriminating between signal and noise down to 0.09% variant allele frequency and an LOD(90) at 0.18%. A superior sensitivity was also confirmed by orthogonal comparison to a commercially available liquid biopsy-based assay for cancer detection.