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).