Integration of genomic data and ecological modelling for demographic history reconstruction: Sauropsida as case studies

Genomic tools have greatly advanced the study of evolutionary history and population demography, particularly when combined with ecological information such as habitat, climate, and species interactions. Integrating genomic data with approaches like Ecological Niche Models (ENMs) allows a deeper understanding of species’ responses to environmental changes, including demographic history, barriers to gene flow, and population dynamics. However, such integrative approaches remain limited, especially across multiple species, and their effectiveness depends on the availability of high-quality reference genomes that enable accurate analyses of genetic variation and evolutionary processes. In this thesis, I describe the development and application of a bioinformatic pipeline for producing high-quality reference genomes and explore how the integration of genomic and ecological data can improve our understanding of evolutionary history and demography in Sauropsida. We implemented a reproducible and accessible pipeline within the Galaxy platform, integrating PacBio HiFi long reads with Hi-C chromatin interaction data and incorporating extensive quality control steps. This approach enables the generation of chromosome-level assemblies as well as fully phased, haplotype-resolved genomes when parental data are available. The pipeline was validated across multiple vertebrate species, demonstrating improved contiguity and overall quality compared to existing assemblies. I then applied this pipeline to generate a high-quality genome for the black-legged kittiwake (Rissa tridactyla), which showed substantial improvements in completeness and chromosomal assignment. Through comparative analyses with other Charadriiformes species, I identified multiple lineage-specific chromosomal rearrangements, suggesting a potential role of chromosome fusions and fissions in diversification. I also produced a chromosome-level genome for the European pond turtle (Emys orbicularis), which I used in comparative analyses across Testudines. By integrating genomic and ecological data, I identified recurrent cycles of population expansion and contraction, with a general decline in effective population size associated with post-glacial cooling, while no clear relationship emerged between genetic diversity and conservation status. Finally, I conducted a broader comparative analysis across Squamata species, revealing similar demographic patterns, with population declines following the Last Glacial Maximum and expansions during warmer periods. Among the life-history traits examined, only body size showed a significant relationship with genetic diversity. Overall, this work highlights the importance of high-quality reference genomes and demonstrates the value of integrating genomic and ecological data to better understand biodiversity, evolutionary processes, and species conservation.