The hypervariable segment I of the control region of the mtDNA (positi
ons 16024-16383) was PCR-amplified from mouth scrape and hairs and seq
uenced in 45 unrelated individuals of pure matrilineal Basque descent.
Twenty-seven different sequences were found, of which 21 are unique t
o the Basques. The allelic partition observed, together with resamplin
g experiments, suggested that much more variation remained to be disco
vered. The mean pairwise difference in number of nucleotides between i
ndividuals was 3.15, a very low value. Moreover, the number of steps f
or the most parsimonious tree is very low compared to the number of di
fferent sequences. Both findings suggest that the Basque population wa
s founded by a few lineages that diverged in a short time span. The nu
mber of nucleotide differences between individuals was shown not to be
influenced by the distance between their birthplaces, thus validating
the sampling strategy used a posteriori. The pairwise difference dist
ribution agreed well with the three-parameter model proposed by Rogers
& Harpending (1992). The parameter estimates found for the Basques im
plied that a demographic expansion (or perhaps two, given the bimodal
shape of the distribution) took place sometime between 14500 and 42000
sp which is in agreement with archaeological data. Our sample was com
pared to other populations for which D-loop sequences were available t
hrough the Nei & Miller (1900) distance. In a neighbour-joining tree,
all the Caucasoid samples, including the Basques, appeared tightly clu
stered, whereas African samples were the most distant to the Caucasoid
s and also the most heterogeneous. Although classical markers, such as
blood groups and protein polymorphisms, clearly separate the Basques
(and the Sardinians) from other European populations, this distinctive
ness was not found using D-loop sequences.