As the "A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages" title implies the European ancestry is in regards to the maternal line specifically.
The article itself in fact clearly supports a Near East paternal lineage:
> the MSY results interpreted plausibly to suggest an overwhelming majority of Near Eastern ancestry on the Ashkenazi male line of descent
As the "A substantial prehistoric European ancestry amongst Ashkenazi maternal lineages" title implies the European ancestry is in regards to the maternal line specifically.
The article itself in fact clearly supports a Near East paternal lineage:
> the MSY results interpreted plausibly to suggest an overwhelming majority of Near Eastern ancestry on the Ashkenazi male line of descent