Browsing by Author "Ba, Yue"

Ringed seals (Pusa hispida) and grey seals (Halichoerus grypus) are known to have hybridized in captivity despite belonging to different taxonomic genera. Earlier genetic analyses have indicated hybridization in the wild and the resulting introgression of genetic material cross species boundaries could potentially explain the intermediate phenotypes observed e.g. in their dentition. Introgression can be detected using genome data, but existing inference methods typically require phased genotype data or cannot separate heterozygous and homozygous introgression tracts. In my thesis, I will present a method based on Hidden Markov Models (HMM) to identify genomic regions with a high density of single nucleotide variants (SNVs) of foreign ancestry. Unlike other methods, my method can use unphased genotype data and can separate heterozygous and homozygous introgression tracts. I will apply this method to study introgression in Baltic ringed seals and grey seals. I will compare our method to an alternative method and assess our method with simulated data in terms of precision and recall. Then, I will apply it to seal data to search for introgression. Finally, I will discuss what future directions to improve our method.