Some broader conclusions for European population history in general:
"The common feature in all three trees is a first split between Southern and Northern Europe with a median time ~7,000 years ago, followed by three more separations close in time ~5,000 years ago between Netherlands, Denmark, Finland and Britain."
Well, 5,000 years ago is 3000 BC, so nice correlation between that and the movement from the East, but what to make of the split between Southern and Northern Europe 5000 BC?
There's also this:
"The relatively recent estimate for the split time between Italy and Spain, ~2,600 years ago, may be a consequence of migration following an earlier separation; the population size of the Italian-Spanish ancestral population was estimated to be extremely large and an upper bound could not be determined, which could be an artifact of ancestral substructure or admixture. Another explanation would be a common source of admixture into both the Spanish and the Italian population, resulting in relatively recent common ancestry."
Here we go again. The programs never seem to produce dates or admixtures that totally work for Southern Europe. 2600 years ago is 600 BC. What common source of migration? In 600 BC northern and central Italy were being hit by the "Celtic" migrations. Does that apply to Spain as well? There was Greek migration to southern Italy but no such large colonization in Spain to my knowledge.
Maybe large population sizes mean just that...large population sizes. That might explain a lot of the difference between what happened in Southern versus Northern Europe.
That 2600 hundred years ago date does square with Ralph and Coop, who give a date of 2500 years ago as the time after which neither Spain nor Italy experienced really significant gene flow from outside.
http://journals.plos.org/plosbiology...l.pbio.1001555