Statistical Evidence for Miscoding Lesions in Ancient DNA Templates

Statistical evidence for miscoding lesions in ancient DNA templates.

It is generally believed that sequence heterogeneity in PCR products from fossil remains are due to regular DNA polymerase errors as well as miscoding lesions compounded by damage in the template DNA (Pääbo 1990; Handt et al. 1994b, 1996; Höss et al. 1996; Krings et al. 1997). However, it has been difficult to test the frequency with which this assumption holds. First, DNA extractions from foss...

Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis

Although ancient DNA (aDNA) miscoding lesions have been studied since the earliest days of the field, their nature remains a source of debate. A variety of conflicting hypotheses exist about which miscoding lesions constitute true aDNA damage as opposed to PCR polymerase amplification error. Furthermore, considerable disagreement and speculation exists on which specific damage events underlie o...

Recharacterization of ancient DNA miscoding lesions: Insights in the era of the GS20

Statistical methods for analyzing ancient DNA from hominins.

In the past few years, the number of autosomal DNA sequences from human fossils has grown explosively and numerous partial or complete sequences are available from our closest relatives, Neanderthal and Denisovans. I review commonly used statistical methods applied to these sequences. These methods fall into three broad classes: methods for estimating levels of contamination, descriptive method...

Statistical guidelines for detecting past population shifts using ancient DNA.

Populations carry a genetic signal of their demographic past, providing an opportunity for investigating the processes that shaped their evolution. Our ability to infer population histories can be enhanced by including ancient DNA data. Using serial-coalescent simulations and a range of both quantitative and temporal sampling schemes, we test the power of ancient mitochondrial sequences and nuc...