On the basis of comprehensive RFLP analysis, it has been inferred that simi
lar to 97% of Native American mtDNAs belong to one of four major founding m
tDNA lineages, designated haplogroups "A"-"D." It has been proposed that a
fifth mtDNA haplogroup (haplogroup X) represents a minor founding lineage i
n Native Americans. Unlike haplogroups A-D, haplogroup X is also found at l
ow frequencies in modern European populations. To investigate the origins,
diversity, and continental relationships of this haplogroup, we performed m
tDNA high-resolution RFLP and complete control region (CR) sequence analysi
s on 22 putative Native American haplogroup X and 14 putative European hapl
ogroup X mtDNAs. The results identified a consensus haplogroup X motif that
characterizes our European and Native American samples. Among Native Ameri
cans, haplogroup X appears to be essentially restricted to northern Amerind
ian groups, including the Ojibwa, the Nuu-Chah-Nulth, the Sioux, and the Ya
kima, although we also observed this haplogroup in the Na-Dene-speaking Nav
ajo. Median network analysis indicated that European and Native American ha
plogroup X mtDNAs, although distinct, nevertheless are distantly related to
each other. Time estimates for the arrival of X in North America are 12,00
0-36,000 years ago, depending on the number of assumed founders, thus suppo
rting the conclusion that the peoples harboring haplogroup X were among the
original founders of Native American populations. To date, haplogroup X ha
s not been unambiguously identified in Asia, raising the possibility that s
ome Native American founders were of Caucasian ancestry.