The driving force behind the transition from a foraging to
a farming lifestyle in prehistoric Europe (Neolithization)
has been debated for more than a century [1–3]. Of particular
interest is whether population replacement or cultural
exchange was responsible [3–5]. Scandinavia holds a unique
place in this debate, for it maintained one of the last major
hunter-gatherer complexes in Neolithic Europe, the Pitted
Ware culture [6]. Intriguingly, these late hunter-gatherers
existed in parallel to early farmers for more than a millennium
before they vanished some 4,000 years ago [7, 8]. The prolonged
coexistence of the two cultures in Scandinavia has
been cited as an argument against population replacement
between the Mesolithic and the present [7, 8]. Through analysis
of DNA extracted from ancient Scandinavian human
remains, we show that people of the Pitted Ware culture
were not the direct ancestors of modern Scandinavians
(including the Saami people of northern Scandinavia) but
are more closely related to contemporary populations of
the eastern Baltic region. Our findings support hypotheses
arising from archaeological analyses that propose
a Neolithic or post-Neolithic population replacement in
Scandinavia [7]. Furthermore, our data are consistent with
the view that the eastern Baltic represents a genetic refugia
for some of the European hunter-gatherer populations.