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Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

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Postmortem miscoding lesions in sequence analysis of human ancient mitochondrial DNA.

Ryan Lamers¹, Shana Hayter, Carney D Matheson

¹Department of Biology, Lakehead University, Thunder Bay, ON, Canada.

Journal of Molecular Evolution

|December 11, 2008

Summary

Ancient DNA (aDNA) analysis is prone to errors from genetic miscoding lesions. This study reveals both hydrolytic and oxidative DNA damage in human remains, with damage type correlating to geographic and environmental factors.

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Area of Science:

Ancient DNA Analysis
Molecular Anthropology
Paleogenetics

Background:

Genetic miscoding lesions introduce inaccuracies in ancient DNA (aDNA) sequence interpretation.
Degradation of DNA in ancient human remains can lead to misincorporations during sequencing.

Purpose of the Study:

To identify and assess genetic miscoding lesions in degraded mitochondrial DNA (mtDNA) from human remains.
To investigate the types and prevalence of DNA damage affecting mtDNA profiles.

Main Methods:

Cloning and direct sequencing of amplified mtDNA from 42 individuals across diverse geographic locations.
Analysis of DNA damage, including hydrolytic and oxidative products.

Main Results:

High levels of hydrolytic damage (56.5%) were observed, with type 2 transitions being common.
Oxidative damage products (43.5%) were also detected, a finding contrasting with previous bone/teeth studies.
Type 2 transversions, indicative of oxidative damage, comprised 30.3% of all miscoding lesions.

Conclusions:

This study reports the presence of oxidative DNA damage in ancient human mtDNA.
The type of DNA damage is specific and correlates with geographic location and taphonomic conditions.