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Cryptic contamination and phylogenetic nonsense.

Linderholm A, Malmström H, Lidén K, Holmlund G, Götherström A - PLoS ONE (2008)

Bottom Line: If it does, the results are rejected as contamination, while if it does not, they are often considered authentic.We show here that human contamination in ancient material may well deviate from local allele frequencies or the distributions to be found among the laboratory workers and archaeologists.We conclude that it is not reliable to authenticate ancient human DNA solely by showing that it is different from what would be expected from people who have handled the material.

View Article: PubMed Central - PubMed

Affiliation: Archaeological Research laboratory, Stockholm University, Stockholm, Sweden. anna.linderholm@arklab.su.se

ABSTRACT
Ancient human DNA has been treated cautiously ever since the problems related to this type of material were exposed in the early 1990s, but as sequential genetic data from ancient specimens have been key components in several evolutionary and ecological studies, interest in ancient human DNA is on the increase again. It is especially tempting to approach archaeological and anthropological questions through this type of material, but DNA from ancient human tissue is notoriously complicated to work with due to the risk of contamination with modern human DNA. Various ways of authenticating results based on ancient human DNA have been developed to circumvent the problems. One commonly used method is to predict what the contamination is expected to look like and then test whether the ancient human DNA fulfils this prediction. If it does, the results are rejected as contamination, while if it does not, they are often considered authentic. We show here that human contamination in ancient material may well deviate from local allele frequencies or the distributions to be found among the laboratory workers and archaeologists. We conclude that it is not reliable to authenticate ancient human DNA solely by showing that it is different from what would be expected from people who have handled the material.

Show MeSH
Frequency of the T allele located 13910bp upstream of the LCT gene.The groups illustrated are the human samples processed in Linköping, the human samples processed in Stockholm/Uppsala, the negative controls containing human DNA from Linköping, and the negative controls containing human DNA from Stockholm/Uppsala. A = Human samples processed in Linköping, B = Non-human samples processed in Linköping, C = Human samples processed in Stockholm/Uppsala and D = Non-human samples processed in Stockholm/Uppsala.
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pone-0002316-g003: Frequency of the T allele located 13910bp upstream of the LCT gene.The groups illustrated are the human samples processed in Linköping, the human samples processed in Stockholm/Uppsala, the negative controls containing human DNA from Linköping, and the negative controls containing human DNA from Stockholm/Uppsala. A = Human samples processed in Linköping, B = Non-human samples processed in Linköping, C = Human samples processed in Stockholm/Uppsala and D = Non-human samples processed in Stockholm/Uppsala.

Mentions: An obvious discrepancy was detected between the results from the three laboratories, the allele frequency for the derived allele (-13910T) in the seven human samples being 0.36 for Linköping and 0.14 for Uppsala and Stockholm (Fig. 3). The frequency of the -13910T allele in modern Sweden is 74% (21), whereas the only published results obtained for archaeological material showed no individuals carrying the -13910T allele in the eight Neolithic samples from Central Europe (16). In this case we observed a difference in allele frequencies in the contaminated samples by contrast with the frequencies expected on the basis of the modern distribution in the country where the material came from and was analysed.


Cryptic contamination and phylogenetic nonsense.

Linderholm A, Malmström H, Lidén K, Holmlund G, Götherström A - PLoS ONE (2008)

Frequency of the T allele located 13910bp upstream of the LCT gene.The groups illustrated are the human samples processed in Linköping, the human samples processed in Stockholm/Uppsala, the negative controls containing human DNA from Linköping, and the negative controls containing human DNA from Stockholm/Uppsala. A = Human samples processed in Linköping, B = Non-human samples processed in Linköping, C = Human samples processed in Stockholm/Uppsala and D = Non-human samples processed in Stockholm/Uppsala.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2384008&req=5

pone-0002316-g003: Frequency of the T allele located 13910bp upstream of the LCT gene.The groups illustrated are the human samples processed in Linköping, the human samples processed in Stockholm/Uppsala, the negative controls containing human DNA from Linköping, and the negative controls containing human DNA from Stockholm/Uppsala. A = Human samples processed in Linköping, B = Non-human samples processed in Linköping, C = Human samples processed in Stockholm/Uppsala and D = Non-human samples processed in Stockholm/Uppsala.
Mentions: An obvious discrepancy was detected between the results from the three laboratories, the allele frequency for the derived allele (-13910T) in the seven human samples being 0.36 for Linköping and 0.14 for Uppsala and Stockholm (Fig. 3). The frequency of the -13910T allele in modern Sweden is 74% (21), whereas the only published results obtained for archaeological material showed no individuals carrying the -13910T allele in the eight Neolithic samples from Central Europe (16). In this case we observed a difference in allele frequencies in the contaminated samples by contrast with the frequencies expected on the basis of the modern distribution in the country where the material came from and was analysed.

Bottom Line: If it does, the results are rejected as contamination, while if it does not, they are often considered authentic.We show here that human contamination in ancient material may well deviate from local allele frequencies or the distributions to be found among the laboratory workers and archaeologists.We conclude that it is not reliable to authenticate ancient human DNA solely by showing that it is different from what would be expected from people who have handled the material.

View Article: PubMed Central - PubMed

Affiliation: Archaeological Research laboratory, Stockholm University, Stockholm, Sweden. anna.linderholm@arklab.su.se

ABSTRACT
Ancient human DNA has been treated cautiously ever since the problems related to this type of material were exposed in the early 1990s, but as sequential genetic data from ancient specimens have been key components in several evolutionary and ecological studies, interest in ancient human DNA is on the increase again. It is especially tempting to approach archaeological and anthropological questions through this type of material, but DNA from ancient human tissue is notoriously complicated to work with due to the risk of contamination with modern human DNA. Various ways of authenticating results based on ancient human DNA have been developed to circumvent the problems. One commonly used method is to predict what the contamination is expected to look like and then test whether the ancient human DNA fulfils this prediction. If it does, the results are rejected as contamination, while if it does not, they are often considered authentic. We show here that human contamination in ancient material may well deviate from local allele frequencies or the distributions to be found among the laboratory workers and archaeologists. We conclude that it is not reliable to authenticate ancient human DNA solely by showing that it is different from what would be expected from people who have handled the material.

Show MeSH