DNA was extracted from similar to 600-year-old human remains found at
an archaeological site in the southwestern United States, and mtDNA fr
agments were amplified by PCR. When these fragments were sequenced dir
ectly, multiple sequences seemed to be present. From three representat
ive individuals, DNA fragments of different lengths were quantified an
d short overlapping amplification products cloned. When amplifications
started from <40 molecules, clones contained several different sequen
ces. In contrast, when they were initiated by a few thousand molecules
, unambiguous and reproducible results were achieved. These results sh
ow that more experimental work than is often applied is necessary to e
nsure that DNA sequences amplified from ancient human remains are auth
entic. Iu particular, quantitation of the numbers of amplifiable molec
ules is a useful tool to determine the role of contaminating contempor
ary molecules and PCR errors in amplifications from ancient DNA.