FIG 2.

Main characteristics and challenges of ancient metagenomic DNA. The original “endogenous” aDNA (i.e., the original DNA in the sample) of a wide range of sample types often makes up only a small fraction of the total genetic content of a sample. Contaminating environmental DNA from close relatives will often reduce confidence in taxonomic profiling and variant calling due to alignment of reads with variants from organisms other than the true ancient organism under investigation. True aDNA has a greater frequency of characteristic C-to-T deamination miscoding lesions at 5′ molecule termini (and a corresponding G-to-A mutation on the complementary 3′ strand of double-stranded libraries). True aDNA fragment distributions typically peak at short lengths, often around 30 to 70 bp, compared to the long lengths of modern DNA.