Ancient genome-based investigation of the dispersal and adaptive evolution of cattle across Eurasia

• Applicant: Professorin Dr. Christina Warinner
• Subject Area: Evolution, Anthropology ; Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
• Term: since 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 551531854

This study aims to comprehensively elucidate the genetic origins and evolutionary history of Eurasian cattle, as well as to unearth Eurasian cattle-specific adaptive evolutionary traits/genes through comparative genomic analysis of ancient and present-day cattle across Eurasia. Specifically, we propose to achieve the following three major objectives. First, it aims to conduct a comprehensive survey of ancient cattle genetic diversity in Inner Eurasia, East Asia, and South Asia, by producing genome sequences of ≥200 ancient cattle. Second, it aims to establish a comprehensive phylogenetic model encompassing major ancient present-day cattle populations including taurine and indicine cattle as well as Eurasian wild aurochs. Third, it aims to identify genes and phenotypes that have conferred adaptive advantages to Eurasian cattle populations to their corresponding local environments. To achieve the objectives of our study, we will organize this project into three work packages (WP). [WP1] We will generate whole genome sequences and/or genome-wide data from over 200 ancient cattle samples from Inner Eurasia, East Asia, and South Asia, including indicine cattle from the Indus Valley Civilization (IVC), to document genetic diversity in these regions across time periods in high resolution. [WP2] Utilizing representative ancient Eurasian cattle populations produced in WP1, we will present phylogenetic models which can adequately explain the genetic relationship among the major taurine and indicine cattle populations in the form of a population graph. The topology of the phylogenetic model will precisely delineate the origins and dispersal routes of and mixtures between Eurasian cattle populations. [WP3] We will identify genes and phenotypes that have undergone adaptive evolution by positive natural selection in each region. On top of novel and standing variation originated in the ancestral taurine cattle population, we will also catalogue genetic elements inherited from Eurasian wild aurochs that had presumably accumulated adaptations to their corresponding environments prior to the introduction of domestic cattle. We believe that the proposed study will provide a significant contribution to the fields of population genetics, archaeology, and agronomic industry. First, it will elucidate the origins and dispersal history of Eurasian cattle in detail, solving a long-standing question in archaeology. Second, it will present a cutting-edge exemplar case on extending paleogenomics beyond human history. Third, it will provide a dynamic example of evolution in action by integrating the effects of dispersal, admixture, natural and artificial selection, and introgression. Last, the historical cattle genetic diversity and adaptive genes found in this study will help livestock industry set up a novel breeding strategy in response to inbreeding depression and rapid climate change.

• DFG Programme: Research Grants
• International Connection: South Korea
• Cooperation Partner: Professor Choongwon Jeong, Ph.D.