Historical DNA damage and contamination
Nucleotide damage estimates for formalin-fixed samples estimated by
mapDamage2 were 3’ G > A = 0.01 (SD = 0.008), and 5’ C
> T = 0.02 (SD = 0.01). Although some human and/or
bacterial contamination was present in all samples, supernatant, pellet,
and RADseq replicates had minor levels of exogenous DNA contamination
with an average of 1.2% (SD = 0.29) 1.1% (SD = 0.5), and 0.71% (SD =
0.14) of reads mapping to non-target genomes respectively. By contrast,
in formalin-fixed replicates mapping rates of reads to exogenous DNA
ranged from 1.4%–81.1% (mean = 25%, SD = 29.2; Fig. 2B).