Ancient DNA has decisively established that there was at least one major demographic shift in Europe between the arrival of the first farmers in the Early Neolithic era and modern Europe. Further ancient DNA data has pretty much pinned this down to the Middle or Late Neolithic era to early Bronze Age time frame. At least in Central and Eastern Europe, this transition very likely involved incoming Indo-Europeans.
There has been great debate over the extent to which this was a peaceful transition (e.g. with the first farmers dying off and leaving a vacuum this is filled peacefully by a second wave of metal using people), or a case of violent conquest. The data is inconclusive, but one recent data point argues for the violent conquest/genocide theory.
A grave containing multiple victims of what appears to have been a violent raid where even women ad children had extremities hacked off in the time frame where this transition took place, suggests that this transition may have been a violent one.
The fact that Indo-European languages replaced earlier ones indicates elite dominance. It is unlikely this occurred through peaceful means even if, in the west, pre-Indo-European genes remained.
There isn't much evidence of violence at the transition in some places. For example, in the IVC, the violence seems to occur at a time of Harappan civilization collapse rather than at a subsequent Indo-European arrival.
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