This is not surprising in retrospect.

The Alps have been a significant barrier to movement throughout European history.

The specific passes through the Alps have been of strategic and commercial importance for exactly this reason: they are the rare exceptions to a generally impassable barrier.

The Alpine communities of the Copper Age, dependent on those passes for connection to the wider world, would naturally have had more limited gene flow than populations in open terrain.

The finding also has implications for understanding how the later steppe migration — the massive population expansion from the Pontic steppe that transformed European genetics between about 3000 and 2500 BCE — affected Alpine communities.