Figure 1. Calcified nodule found among the skeletal remains at Troy.
(A) Burial x24.177 (grave 14, cemetery in quadrat x24). Photo credit Gebhard Bieg, 2005. (B) Cross-section of nodule (sample no x24.177), photo credit: Pathologie Nordhessen 2009. Scale represents 1 cm. (C) Location of Troy. Modern day Turkey is shaded in gray.
Figure 1—figure supplement 1. Map of Troy showing the cemetery in Grid Square x24 and areas of excavation 1988–2012.
Areas of excavation are in gray and the cemetery is marked with a red square. North is at the top of the plan.
Figure 1—figure supplement 2. Metagenomic profiles of shotgun DNA libraries from nodules, based on BLAST analysis of all reads >35 bp length.
(A) Nodule one (Nod1_1h-UDG), 28,713,282 reads total (B) Nodule two (Nod2-UDG), 6,038,994 reads total.
Figure 1—figure supplement 3. Fragment length distributions for non-UDG treated human mitochondrial assemblies.
These FLDs were generated from the Ulna enriched libraries (A + B) as well as the non enriched nodule (C) using mapDamage2 (Jonsson et al., 2013) from merged nonUDG data sets assembled to the human mitochondrial reference genome (Andrews et al., 1999), NCBI accession NC_012920.
Figure 1—figure supplement 4. Ancient DNA damage assessment of human mitochondrial reads.
Damage profiles of non-UDG treated (‘nonU’) as well as UDG treated merged reads assembled to the human mitochondrial rCRS reference genome (NC_012920) for (A) Ulna_Enr1-nonU round one human mitochondrial enrichment, (B) Ulna_Enr2-nonU round 2, and (C) a Nod1_1h-UDG reads (which have been UDG treated). Damage profiles were generated using mapDamage2.(Jonsson et al., 2013).
Figure 1—figure supplement 5. Ancient DNA damage assessment of reads mapped to hg38 chrX, chrY and autosomes.
Damage profiles generated using mapDamage2 (Jonsson et al., 2013) of non-UDG treated (‘nonU’) reads from the NOD1_nonU and NOD2_nonU data set (total of 1,468,381 trimmed and merged reads) with minimum 35 bp length and map quality 30, mapping to (A) hg38 chrX, and (B) hg38 chrY and C) hg38 autosomes.
Figure 1—figure supplement 6. Haplogroup U3 Bayesian Maximum Clade Credibility tree.
Complete human mtDNA genomes assigned to haplogroup U3 (n = 137) were collected from GenBank and aligned with the Troy consensus sequence (highlighted in red). Tree was generated using BEAST v 1.856 and TreeAnnotator.57 Posterior probabilities are shown at nodes.
Figure 1—figure supplement 7. Heatmap of most common taxa in metagenomic samples.
The heatmap gives the log of the frequency of the most common taxa in each sample along the diagonal (if the most frequent is already shown, then second most frequent is added for that sample; Nares and Ear, Nod1_1h-UDG and Nod2-UDG). The taxa in order are - 76775, Malassezia restricta; 76773, Malassezia globosa; 729, Haemophilus parainfluenzae; 60133, Prevotella pallens; 28117, Alistipes putredinis; 47770, Lactobacillus crispatus; 562, Escherichia coli; 487, Neisseria meningitidis; 2001, Streptosporangium roseum; 29385, Staphylococcus saprophyticus; 2702, Gardnerella vaginalis.
Figure 1—figure supplement 8. PCA of Human Microbiome Project and ancient metagenomic taxa.
Taxa were identified using LMAT. PCA performed using prcomp function in R. Legend indicates the origin of the category and the number of samples combined into each category. The first principal component axis separates the placental and ancient samples from the remaining samples. The second principal component axis separates the Sediment-UDG and Ulna-UDG data sets, which likely contain soil contamination, from the remaining samples.
Figure 1—figure supplement 9. Sketch of skeletal preservation.
