Biology subjects

Reisser, C.

Publications and source records attributed to Reisser, C..

6 recordsLinked to original sources

bioRxiv2026

Parallel differentiation extends beyond chromosomal inversions to small genomic islands on a background of rampant gene flow in the European flat oyster (Ostrea edulis)

Heterogeneous genomic landscapes of differentiation can reveal evolutionary processes acting over different timescales. Whereas genetic structure in the European flat oyster, Ostrea edulis, is mainly shaped by geography, previous work suggested parallel differentiation between western and eastern Mediterranean populations and between Atlantic and North Sea populations, resulting in genetic convergence between range margin populations in some genomic regions. Here, we analyzed 27 oysters from four locations using moderate-coverage (~20X) short-read whole-genome sequencing. We first examined three known chromosomal inversions and found evidence that they predate divergence with the sister species O. chilensis. We then scanned the genome for parallel differentiation at the individual-SNP rather than sliding-window scale using the product of allele-frequency differences across the two geographic contrasts. Two of the three inversions were detected, but we also identified 12 small non-inverted genomic regions showing even stronger signals of parallel differentiation. These 'islands of parallelism' typically overlap one or a few genes, and most showed elevated dXY consistent with long-term barriers to gene flow. Two islands overlap nuclear ATP synthase subunits, while mitochondrial ATP8 shows a convergent amino-acid change, suggesting possible nuclear-nuclear and mitonuclear incompatibilities. Finally, demographic inference with heterogeneous gene flow supported post-glacial secondary contact and a lineage-based rather than geography-based population topology. Our results suggest that the genomes of O. edulis lineages have been largely porous to gene flow upon secondary contact, except for chromosomal inversions and small genomic islands. These regions likely act as barrier loci, preserving a signal of a shared evolutionary history among marginal populations that has otherwise been erased by rampant gene flow.

evolutionary biology↗

bioRxiv2026

A cryptic local genetic cluster in Northern France amid the European mosaic of flat oyster lineages revealed by integrating SNP array and whole-genome sequencing

The European flat oyster (Ostrea edulis), like numerous other oyster species, has been exploited for millennia and cultivated and translocated for centuries. Following a severe population decline, and in the context of ongoing conservation and restoration programs, genetic considerations must now be addressed to avoid mistakes. The objective of our study was to complement population genetic studies conducted at various scales along European coasts. Our sampling primarily targeted the French Atlantic, English Channel, and Mediterranean coasts, aiming to provide a fine-scale genetic characterization of populations in these regions. By integrating SNP array and low-coverage sequencing datasets, we obtained a comprehensive overview of the population genetic structure of Ostrea edulis across western Europe. Most previously identified clusters in Western Europe were confirmed. In France, populations assigned to these clusters exhibited notable within-patch homogeneity. However, two key findings emerged: (1) an extensive overlap zone between the Atlantic and western Mediterranean clusters, spanning at least from southern Portugal to southern France, and (2) the detection of a novel, clearly distinct cryptic cluster east of the English Channel, whose geographic range remains to be better delineated. These insights are critical for informing management decisions, particularly as restoration and conservation plans are currently being implemented across the species range.

genetics↗

bioRxiv2026

Genome-Environment Associations reveal shared and unique adaptive loci across multiple pollutants and populations of the eastern mosquitofish Gambusia holbrooki

Rapid adaptation to human-induced stressors is commonplace in the context of global change, including during biological invasions. Identifying the genomic bases and associated biological functions underlying such adaptation is hence crucial to understand and anticipate the response of populations and species to changing conditions. In particular, the extent to which genetic responses to multiple anthropogenic stressors vary between populations in the wild has been relatively unexplored. We addressed this question by leveraging whole-genome sequence data (both PoolSeq and IndSeq) in invasive populations of Gambusia holbrooki - a widespread invasive fish species - collected from 14 locations with different multi-pollutants exposure. We sought to identify adaptive loci associated with pollution tolerance by conducting Genome-Environment Association (GEA) analyses. Additionally, we investigated the degree of adaptive loci reuse between pollutants and their combinations as well as across populations. We found strong signals of association between allele frequency changes and pollutant exposure at several genomic locations, often overlapping with genes known for their functions in detoxification and immune response. We further showed that most adaptive loci are not shared among all populations, suggesting heterogeneous genomic response to each local selection. Interestingly, multiple tests looking for footprints of selection and association to pollutants yielded consistent results. Our results shed new light on the extent of genetic convergence in the genomic bases of rapid adaptation to different cocktails of human-induced pollution, and are important to our understanding of the fate of wild populations facing increasingly complex and stressful environments.

genomics↗

bioRxiv2024

Transcriptomic and Biochemical analysis of Procambarus clarkii upon exposure to Pesticides: Population-Specific responses as a sign of pollutant resistance?

The effects that anthropogenic stressors may have on modulating species plasticity has been relatively unexplored; however, it represents a scientific frontier that may offer insights into their ability to colonize new habitats. To explore the advantage that inhabiting polluted environments may offer to invasive species, we selected the crayfish Procambarus clarkii, a species that can colonize and thrive in a wide range of aquatic environments, including heavily polluted ones. Here, we studied the molecular and physiological responses of crayfish when experimentally exposed to a pesticide mix of azoxystrobin and oxadiazon at sublethal concentrations. We compared these responses in three isolated crayfish populations in Southern France that are established in areas with different pollution levels: a) Camargue, seasonally affected by pesticide pollution; b) Bages-Sigean, impacted all year-round by domestic effluents and; c) Salagou, a more pristine site. Gene expression analyses revealed that the response to the pesticide mix was the strongest in the Camargue crayfish. In this population, a total of 88 differentially expressed genes (DEGs) were identified in hepatopancreas and 78 in gills between exposed and control laboratory groups. Among genes that were differentially expressed and successfully annotated, those involved in stress, DNA repair, immune response, and translation and transcription processes stand out. Interestingly, the hepatopancreas responded mainly with upregulation, but with downregulation in the gills. This suggests that compared to naive individuals, when exposed to these biocides in their natural habitat crayfish respond with different mechanistic strategies that may confer them adaptability at the population level. Responses in terms of antioxidant and detoxification enzymes also corroborate differences to biocide inputs according to the origin of the crayfish.

molecular biology↗

bioRxiv2018

Whole transcriptome sequencing and biomineralization gene architecture associated with cultured pearl quality traits in the pearl oyster, Pinctada margaritifera

BackgroundCultured pearls are unique gems produced by living organisms, mainly molluscs of the Pinctada genus, through the biomineralization properties of pearl sac tissue. Improvement of P. margaritifera pearl quality is one of the biggest challenges that Polynesian research has faced to date. To achieve this goal, a better understanding of the complex mechanisms related to nacre and pearl formation is essential and can now be approached through the use of massive parallel sequencing technologies. The aim of this study was to use RNA-seq to compare whole transcriptome expression of pearl sacs that had producing pearls with high and low quality. For this purpose, a comprehensive reference transcriptome of P. margaritifera was built based on multi-tissue sampling (mantle, gonad, whole animal), including different living stages (juvenile, adults) and phenotypes (colour morphotypes, sex).\n\nResultsStrikingly, few genes were found to be up-regulated for high quality pearls (n = 16) compared to the up-regulated genes in low quality pearls (n = 246). Biomineralization genes up-regulated in low quality pearls were specific to prismatic and prism-nacre layers. Alternative splicing was further identified in several key biomineralization genes based on a recent P. margaritifera draft genome.\n\nConclusionThis study lifts the veil on the multi-level regulation of biomineralization genes associated with pearl quality determination.

molecular biology↗

bioRxiv2018

Identification of general patterns of sex-biased expression in Daphnia, a genus with environmental sex determination

Daphnia reproduce by cyclic-parthenogenesis, where phases of asexual reproduction are intermitted by sexual production of diapause stages. This life cycle, together with environmental sex determination, allow the comparison of gene expression between genetically identical males and females. We investigated gene expression differences between males and females in four genotypes of Daphnia magna and compared the results with published data on sex-biased gene expression in two other Daphnia species, each representing one of the major phylogenetic clades within the genus. We found that 42% of all annotated genes showed sex-biased expression in D. magna. This proportion is similar both to estimates from other Daphnia species as well as from species with genetic sex determination, suggesting that sex-biased expression is not reduced under environmental sex determination. Among 7453 single copy, one-to-one orthologs in the three Daphnia species, 707 consistently showed sex-biased expression and 675 were biased in the same direction in all three species. Hence these genes represent a core-set of genes with consistent sex-differential expression in the genus. A functional analysis identified that several of them are involved in known sex determination pathways. Moreover, 75% were overexpressed in females rather than males, a pattern that appears to be a general feature of sex-biased gene expression in Daphnia.\n\nShort summaryIn some species with environmental sex determination, gene expression can be compared between genetically identical males and females. Here, we investigated sex-biased expression in one such species, D. magna, and compared it with data from two congeners. We found that all three species have a common set of 675 genes with consistent differential expression and with a strong bias towards overexpression in females rather than males. Moreover, the proportion of sex-biased genes in each of the three Daphnia species was similar to Drosophila species with genetic sex determination, suggesting that sex-biased expression is not necessarily reduced under environmental sex determination.

genomics↗