3.1 Metagenomics
For the stomach DNA sample of the Llullaillaco summit mouse, we sequenced a total of 423,477,275 reads, yielding 127,043 Mbases, with 92.48% of reads ≥ q30 and a mean quality score of 35.69. We assembled a total of 9,138 contigs ≥1,000 bp in length (21,188,348 bp), with a maximum length of 103,345 bp. Out of 991 contigs that were identified at the order level and above, the vast majority were assigned to super kingdom Bacteria (699 contigs), with Proteobacteria (563 contigs) and Firmicutes (99) as the dominant phyla. Only 1.3% of contigs (n =13) were assigned to plants (clade Streptophyta, class Magnoliopsida [= dicotyledons]), and all were assigned to a single representative of the coca family, Erythroxylaceae (Erythroxylum novagranatense ). This shrub species is widely cultivated in South America because its leaves are a rich source of the psychoactive alkaloid, cocaine. In the stomach contents of the summit mouse, we detected no traces of DNA from arthropods nor from vicuña, guanaco, or other potentially co-distributed Andean mammals.