In population genetics, making an accurate calling and phasing of genetic variants is crucial, but it is often a non-trivial challenge, especially for non-model organisms with modest sequencing coverage (<10X). This project is set to tackle these challenges by testing different methods and approaches for imputing and phasing genomic datasets in endangered bird species. Anchored by a large dataset from a bottlenecked species, the project will leverage a high-depth (>40X) dataset of founders’ (historical) genomes, together with hundreds of lower-depth sequencing of the descendants’ (contemporary) genomes. Theoretically, precise phasing and variant calling in the founder genomes should facilitate confident imputation in contemporary genomes. The approach is further bolstered by the known pedigrees of these populations, offering a prime opportunity to validate and refine these methods.
Data available for this project includes pedigrees, hundreds of whole genomes, and chromosome-level assemblies for three endangered bird species. This dataset not only supports the core objectives of this study but also opens avenues for exploring evolutionary patterns and conservation in these species.
Profile: We seek a student with a strong foundation in bioinformatics, complemented by a keen interest and understanding of population genetics and evolutionary genomics. This project offers the opportunity to contribute to the conservation efforts of endangered species through the lens of cutting-edge genetic analysis, providing valuable insights into their evolutionary trajectories.
Contact: Hernán E. Morales, hernan.morales@biol.lu.se