How did diseases influence human evolutionary processes in Africa? And what is the ‘Pleistocene disease baseline’?

Since post-mortem DNA decays rapidly without the enzymatic repair mechanisms of living cells, characteristic features of aDNA (and sedaDNA) include 1) short DNA fragment length (˂150 bp), 2) increased rate of cytosine (C) to thymine (T) substitutions close to the ends of fragments and 3) increased occurrence of purines (adenine (A) and guanosine (G) residues) before strand breaks. While, like other types of biomolecules, DNA can persist long after the death of the source organism, the preservation of aDNA molecules in anthropogenic sediments is dependent on various physical, chemical and biological sedimentary conditions (i.e. taphonomy, oxygenation, microbial diagenesis, pH levels and ionic strength and the presence of cations, humics and humates). Accordingly, two major factors influence the reliability of DNA sequences obtained from ancient samples. These are 1) contamination with modern DNA and 2) DNA damage that changes the sequence of the ancient DNA. 

Detailed descriptions of how we will address issues concerning contamination and aDNA fragmentation are provided under the 'Lab Notes' heading.