“…The development of DNA library construction methods that exploit molecular features of aDNA, in particular the presence of damage in the form of single-strand breaks [86] and/or deaminated cytosines [87], has also enhanced our ability to access aDNA templates. Finally, target enrichment approaches, aimed at the characterization of organellar DNA [88] or of a limited number of mitochondrial and nuclear loci [89], or up to hundreds of millions of SNPs scattered throughout the nuclear genome [90] and even of the entire nuclear genome [91, 92], now contribute to the retrieval of the genome-scale information required to address major biological questions in both a cost- and time-effective manner. It is worth noting that a number of computational approaches have also helped to quantify DNA damage [93, 94], to reduce its impact on downstream analyses [94, 95], and to improve the sensitivity and accuracy of aDNA read alignments [96–99].…”