Covid19 has delayed some aspects of the project and forced us to adapt to the new situation. Specifically, we have not been able to sequence as many samples as we planned. We therefore progressed by first optimizing some of the bioinformatics and population genetics methods and pipelines we would need for the Bos data, using a different whole-genome data set available to us as training data. In addition, we have managed to secure and analyze whole-genome data from a large set of cattle from around the World and domesticated banteng (also known as Bali cattle), as well as from a small number of wild Bos individuals. We have analyzed these data using the pipelines mentioned above and found surprisingly large amounts of introgression from banteng into the domestic cattle breeds. Following this finding we have worked on identifying regions of the genome that have exceptionally high proportions of banteng ancestry in the breeds that have experienced introgression, as these are candidates of adaptive introgression, or introgressed regions that have been co-opted by selection in the receiving cattle populations. This is a very important part of what BOSADMIX aims to achieve. We are currently working to understand the types of selection acting on regions introgressed from banteng into cattle, and the historical details such as time and place of admixture.
Moreover, we have managed to get access to a set of museum samples, which we have DNA extracted and sequenced. These represent a wide geographical range of both banteng and gaur, the two wild Bos species that are most severely lacking in existing genome data. These samples will be most valuable in a broader analysis of where and when admixture has occurred between different Bos species, which introgressed elements have been retained in recipient populations and what their functions are.
