Return of wolves to Europe raises concerns where conservation efforts collide with interests of other industries. The stakeholders agree that wolf/dog hybrids should be removed from populations. Genetic methods based on short tandem repeat genotyping are reliable only in detecting up to second generation hybrids. Individuals with admixed genome can be identified with whole-genome genotyping.

The student will download publicly available sequencing reads of wolves (Canis lupus) and supplement the dataset with up to 50 dogs. They will trim and filter the reads based on quality and map them onto a dog reference genome to call single nucleotide polymorphisms. Selecting sites with substitutions for which there are homozygots for reference and alternative alleles, the student will polarise the genomic dataset. They will assess hybridisation between wolves and dogs, identifying individuals of hybrid descend. Using the polarised genomes, the student will infer genomic regions introgressing into the wolf genome from the genepool of domestic dogs, and interpret the results.

Literature:

Anderson et al. (2009). Molecular and evolutionary history of melanism in North American gray wolves. Science, 323, 1339–1343.

Baird, S. J. E., Petružela, J., Jaroň, I., Škrabánek, P., Martínková, N. (2023). Genome polarisation for detecting barriers to geneflow. Methods in Ecology and Evolution, 14, 512–528.