Data from: Y chromosome sequences reveal a short Beringian Standstill, rapid expansion, and early population structure of Native American founders

The Americas were the last inhabitable continents to be occupied by
humans, with a growing multidisciplinary consensus for entry 15-25
thousand years ago (kya) from northeast Asia via the former Beringia land
bridge. Autosomal DNA analyses have dated the separation of Native
American ancestors from the Asian gene pool to 23 kya or later, and mtDNA
analyses to ~25 kya, followed by isolation (‘Beringian Standstill’) for
2.4-9 ky and then a rapid expansion throughout the Americas. Here, we
present a calibrated sequence-based analysis of 222 Native American and
relevant Eurasian Y chromosomes (24 new) from haplogroups Q and C, with
four major conclusions. First, we identify three to four independent
lineages as autochthonous and likely founders: the major Q-M3 and rarer
Q-CTS1780 present throughout the Americas, the very rare C3-MPB373 in
South America, and possibly C3-P39/Z30536 in North America. Second, from
the divergence times and Eurasian/American distribution of lineages, we
estimate a Beringian Standstill duration of 2.7 ky or 4.6 ky according to
alternative models, and entry south of the ice sheet after 19.5 kya.
Third, we describe the star-like expansion of Q-M848 (within Q-M3)
starting at 15 kya in the Americas, followed by establishment of
substantial spatial structure in South America by 12 kya. Fourth, the deep
branches of the Q-CTS1780 lineage present at low frequencies throughout
the Americas today may reflect a separate out-of-Beringia dispersal after
the melting of the glaciers at the end of the Pleistocene.