In this thesis, I present works related to population genetics in non-model organisms in the form of a methodological paper and an application to whole genome sequence (WGS) in cattle manuscript. Both expand our knowledge in evolutionary biology by investigating different aspects of WGS data analyses.
In the first published paper, we developed a method to jointly determine sample sex and sex-linked scaffolds from low depth WGS data. Our method works with high accuracy in mammals and birds with a wide range of sample sizes and genome assemblies. We validated our approach under extreme scenarios of very low depth genomic data, unbalanced sex ratio, and explored the limitations of genome assembly quality.
The second manuscript is based on WGS of Indonesian cattle breeds, which have a mixed zebu (Bos indicus) and banteng (Bos javanicus) ancestry. We inferred various degrees of banteng ancestry in different breeds, and identified a breed with a surprising high level of genetic diversity, Madura cattle, poses the highest amounts of banteng introgression among other local breeds. We also inferred the admixture time, which aligns with previous historical records of around 1200-1500 years ago. We used our admixture and population structure analyses to hypothesize a history of origin of the Indonesian cattle from multiple Asian Bos sources. We also identified genes under positive selection in introgressed regions, as a potential signature of adaptive introgression, both in individual breeds and across breeds.
Our manuscript provides new results on the globally significant population of cattle found in Indonesia, and furthermore provides a list of important novel genetic variants which until now were an unknown resource of genetic diversity in cattle.