Archaeogenetics has revealed two major migrations that shaped European prehistory; one starting in the 7th millennium BCE and associated with the transition to agriculture, and another with the appearence of the Corded Ware cultural complex in the early 3rd millennium BCE. However, most findings have come from studies employing a continent-wide and/or low regional density sampling approach, leaving many temporal and geographic gaps in the current European archaeogenetic record. In order to build upon previous studies, this thesis employed a high-density sampling approach to study the population structure of Neolithic to Bronze Age central Europe in finer detail. In total, genome-wide ancient DNA was analysed from 283 newly reported individuals from present-day Bohemia, Czech Republic. In doing so, new insights into population structure, genetic turnovers, and social processes were discovered and discussed. These include a genetic turnover between the Jordanow and Funnelbeaker cultural groups, a genetic turnover between Early and Late Corded Ware groups, and a genetic turnover between Bell Beaker and Únětice groups. Insights into social structure and processes revealed the likely contacts between early farming communities with hunter-gatherer groups of Eastern Europe, that the integration of pre-Corded Ware people into Corded Ware society was likely a sex-biased process, and the emergence of a strict patrilineal social system in Late Corded Ware and Bell Beaker cultural groups which broke down with the appearance of early Únětice cultural groups. Insights from a detailed investigation into an Early Bronze Age cemetery from Mikulovice revealed a genetically homogeneous group with evidence of patrilocality and families spanning up to four generations. This thesis shows the potential of more detailed, higher-resolution studies to reveal previously unknown genetic structure and social processes.