The absence in South American aboriginals of an Asian-specific marker,
a 9-bp deletion between the genes for the second subunit of cytochrom
e oxidase II and lysine transfer RNA in region V, has been interpreted
as a bottlenecking effect at the Isthmus of Panama during the peoplin
g: of the Americas. We screened mitochondrial DNA (mtDNA) for this 9-b
p tandem repeat and for polymorphisms in specific regions of the mtDNA
in 2 ancient and 31 contemporary samples from South American aborigin
als. We found additional (mtDNA) diversity in South American aborigina
ls in three ways. First, an Asian-specific marker not previously repor
ted in South American aboriginals was identified by a sequencing analy
sis in both the contemporary Andean and Amazonian aboriginal peoples.
Second, two new haplotypes so far unique to South American aboriginals
were found. Additionally, we show that South American aboriginals fal
l into discrete populations. These results suggest that the prehistori
c colonization of South America is the outcome of multiple migrations;
the data do not support a bottlenecking effect at the Isthmus of Pana
ma.