Sophie Valk

The European flat oyster (Ostrea edulis) is an ecologically and economically important bivalve that has been subjected to a long history of human exploitation. By forming biogenic reefs, O. edulis plays a key role in providing benthic habitat and thereby contributes to overall marine biodiversity. Rapid population declines from the beginning of the 20th century have incentivized restoration initiatives to restore flat oyster populations and their habitats. Since then, a growing number of studies focused on the genetic characterization of O. edulis, revealing phylogeographical population structure across its native distribution range. However, as outlined in Chapter 1, most genetic studies cover large spatial scales and therefore fail to capture fine-scale genetic population structure. Moreover, the majority of research has focused on single-nucleotide polymorphisms (SNPs), the most commonly studied form of genetic variation. Other sources of variation, such as structural variants (SVs), remain comparatively understudied despite their potential to reveal evolutionary dynamics relevant for restoration. This thesis therefore aims to fill this fundamental knowledge gap by elucidating intraspecific (epi)genetic diversity of O. edulis in a restoration context.

In Chapter 2, genetic population structure was assessed among local Dutch populations in the context of restoration efforts by genetically comparing foreign and locally cultured individuals with wild Dutch oysters. The remaining Dutch wild populations comprised a genetically diverse panmictic cluster with high gene flow. In contrast, foreign populations used as a source in Dutch restoration projects exhibited genetic divergence from wild populations. Although hatchery-produced oysters displayed high genetic similarity with Dutch wild oysters, elevated levels of kinship highlight the potential risk of inbreeding. Accordingly, future restoration strategies involving the supplementation of degraded reefs with translocated foreign or locally cultured oysters require careful consideration to optimize restoration effectiveness while preserving genetic diversity.

In addition to single-nucleotide variation, SVs represent an important source of genetic diversity, with recent advances in long-read sequencing and bioinformatic enabling their comprehensive characterization. In Chapter 3, the SV landscape of the O. edulis genome was characterized, demonstrating that SVs complement SNPs in capturing genetic diversity and population structure. In addition, overlap with repeat elements revealed the activity of repeats in generating genome-wide variation. Previously identified chromosomal inversions exhibited elevated densities of SVs and SNPs, suggesting that inversions act as reservoirs of genetic variation and may facilitate local adaptation. Overall, SVs play a key role in shaping genomic population structure, highlighting their relevance for the conservation of O. edulis.

Beyond genetic variation, epigenetic variation contributes to phenotypic plasticity by influencing (post-)transcriptional gene regulatory mechanisms. Sex reversal, one such plastic trait, is primarily driven by environmental factors and complicates culturing of O. edulis for restoration purposes. In Chapter 4, the association between epigenetic mechanisms and sex reversal was assessed by comparative analysis of genome-wide patterns of DNA methylation in gill tissue across sex phenotypes. This revealed hermaphrodite oysters displayed a distinct DNA methylation profile compared to male and female oysters, likely reflecting epigenetic remodeling involved with regulating energy homeostasis and metabolism following sex reversal.

Following characterization of sex-specific DNA methylation across sex phenotypes in Chapter 4, Chapter 5 adopts a machine learning approach to select epigenetic markers for sex classification. The 14 proposed markers enabled classification of hermaphrodite versus non-hermaphrodite oysters, and distinguished male-biased from female-biased oysters with moderate accuracy. Upon further validation, these markers pave the way for studying sex reversal in live oysters, with important implications for culturing O. edulis.

Advances in sequencing approaches and bioinformatic pipelines have expanded the scope of molecular research, enabling assessment of ecosystem biodiversity and functioning in less invasive and time-consuming ways compared to morphological methods. Chapter 6 explored how molecular approaches can be integrated into standardized monitoring frameworks. By taking an ecosystem-wide perspective, current molecular approaches for assessing North Sea biodiversity and ecosystem functioning were reviewed. Additionally, challenges and areas of improvement are discussed, providing a baseline understanding of the current state of molecular monitoring. Recommendations for integrating these tools into standardized marine monitoring programs of North Sea biodiversity are expected to support management and restoration of North Sea ecosystems.

In addition to the fundamental characterization of the (epi)genetic architecture of O. edulis in a restoration context (obtained in Chapters 2 – 5), it is essential that these molecular insights inform applied oyster restoration strategies to optimize restoration effectiveness while preserving genetic diversity. Therefore, the final chapter (Chapter 7) discussed how molecular insights into population structure and evolutionary dynamics can be integrated in active oyster restoration. An integrative roadmap is presented, offering practical guidelines for incorporating molecular insights into locally tailored restoration strategies to support the effective and sustainable restoration of O. edulis and their biogenic reef habitats.