The continental origins of Japanese Y haplogroups
Given that we have identified putative Y chromosome
markers of Jomon (or pre-Jomon) and Yayoi migrations,
can we trace the origins of these lineages before
they entered Japan? We infer that the Japanese have at
least two lineages (D-P37.1 and C-M8) that descend
from Paleolithic founders. Evidence from SNPs and
STRs (Table 2) suggests that both lineages have great
genealogical depth. In the case of haplogroup D, a
striking number of point mutations have accumulated
on this Japanese lineage (Fig. 2). The divergence of the
Japanese D lineage implies a very early period of dispersal
into the Japanese archipelago followed by a long
period of isolation from populations on the mainland.
There is only one other lineage that exhibits more
mutations along an internal branch on the Y chromosome
haplogroup tree (YCC 2002; Jobling and Tyler-
Smith 2003). This branch, A2, is found among the
Khoisan of Namibia, a population that also may have
been isolated for a very long period of time (Hammer
et al. 2001; Wilder et al. 2004).
The highest frequency of continental D lineages is
found in central Asia (Fig. 2), especially in Tibet
(50.4%). Evidence for shared ancestry between Tibetans
and Japanese is seen in the MDS plot (Fig. 3). We
hypothesize that the area between Tibet and the Altai
Mountains in northwestern China is the primary
candidate region for the geographic source of Paleolithic
Japanese founding Y chromosomes. Although Tibetans
and people from the Altai have D lineages that are differentiated
from those in Japan, there are still ‘‘ancestral’’
chromosomes that are not marked by any known
mutations on the D lineage in Tibet and the Altai
(Fig. 2). Historical records suggest that Tibetan populations
were derived from ancient tribes of northwestern
China that subsequently moved to the south and admixed
with southern natives in the last 3,000 years (Ruofu
and Yip 1993; Cavalli-Sforza et al. 1994; Wen et al.
2004). The survival of ancient lineages within haplogroup
D in Tibetans and Japanese may well reflect long periods
of isolation for both groups. Interestingly, a Y-SNP
survey of Andaman Islanders found a very high frequency
of haplogroup D-M174* chromosomes in this
isolated population that likely descends from Paleolithic
Asian ancestors (Thangaraj et al. 2003). Recent expansions
and population replacements in Asia, perhaps
associated with the spread of agriculture, may have led to
the near extinction of haplogroup D in other Asian
populations.