Biology subjects

Lapegue, S.

Publications and source records attributed to Lapegue, S..

4 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↗

bioRxiv2025

k-mer spectra and allelic coverage analyses reveal pervasive polymorphic duplications in Ostrea edulis

Oysters are known for their high genetic diversity, potentially high genetic load, and structurally complex genomes. The European flat oyster, Ostrea edulis, is no exception. Here, we combined a reference-free analysis of pairs of k-mers differing by a single nucleotide (hereafter: het-mers) with a reference-based analysis of allelic coverage using high-coverage short-read sequencing data (70-160X) from five individuals. Up to one-third of SNPs called as heterozygous within an individual exhibited allelic coverage fractions departing from the expected 0.5 ratio. Despite no evidence of recent whole-genome duplication, 40% of het-mers displayed coverage profiles consistent with duplicated genomic segments. We classified AAB het-mers as CN3 and AAAB or AABB het-mers as CN4, corresponding to nucleotide variants located within segments present in three and four copies, respectively, and interpreted as heterozygous and homozygous duplications. These CN3 and CN4 het-mers were typically observed in only a subset of individuals and mostly switched among CN3, CN4, or absence from the het-mer catalog, providing evidence for pervasive paralogous variants associated with rampant polymorphic duplications of genomic segments that vary in copy number among individuals. Reference-based analysis of sequencing depth and allelic coverage fraction similarly showed that SNPs with deviant allelic coverage are frequently associated with duplicated genomic segments segregating within populations, predominantly at low frequencies. Despite their different principles and potential biases, both approaches converged on a minimum estimate of 15% of nucleotide variants being associated with polymorphic duplications. Duplication-associated SNPs occurred in coding and non-coding regions to a similar extent, but their distribution was heterogeneous across chromosomes, with the highest densities on three of the ten chromosomes. These three chromosomes are non-metacentric and particularly prone to chromosome loss in oysters, which are known for their high incidence of somatic aneuploidy. This pattern supports two non-exclusive hypotheses: an architecture-driven model in which chromosome properties prone to structural instability promote both duplications and somatic aneuploidy, and a compensation-driven model in which duplications evolve to buffer dosage imbalance in aneuploid cells. Finally, we discuss how extensive polymorphic duplication may bias population genomic analyses in O. edulis and other ostreids.

genomics↗

bioRxiv2018

Analysis of genome-wide differentiation between native and introduced populations of the cupped oysters Crassostrea gigas and Crassostrea angulata

The Pacific cupped oyster is genetically subdivided into two sister taxa, Crassostrea gigas and C. angulata, which are in contact in the north-western Pacific. The nature and origin of their genetic and taxonomic differentiation remains controversial due the lack of known reproductive barriers and morphologic similarity. In particular, whether ecological and/or intrinsic isolating mechanisms participate to species divergence remains unknown. The recent co-introduction of both taxa into Europe offers a unique opportunity to test how genetic differentiation maintains under new environmental and demographic conditions. We generated a pseudo-chromosome assembly of the Pacific oyster genome using a combination of BAC-end sequencing and scaffold anchoring to a new high-density linkage map. We characterized genome-wide differentiation between C. angulata and C. gigas in both their native and introduced ranges, and showed that gene flow between species has been facilitated by their recent co-introductions in Europe. Nevertheless, patterns of genomic divergence between species remain highly similar in Asia and Europe, suggesting that the environmental transition caused by the co-introduction of the two species did not affect the genomic architecture of their partial reproductive isolation. Increased genetic differentiation was preferentially found in regions of low recombination. Using historical demographic inference, we show that the heterogeneity of differentiation across the genome is well explained by a scenario whereby recent gene flow has eroded past differentiation at different rates across the genome after a period of geographical isolation. Our results thus support the view that low-recombining regions help in maintaining intrinsic genetic differences between the two species.

evolutionary biology↗