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BRS1 BRS2 BRS3 BRS4 BRS5 Total BRS1 BRS2 BRS3 BRS4 BRS5 Aconoidasida Babesia Bovis Protozoan Parasite 0 0 59 45 820 0 924 43.8

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BRS1 BRS2 BRS3 BRS4 BRS5 Total BRS1 BRS2 BRS3 BRS4 BRS5 Aconoidasida Babesia Bovis Protozoan Parasite 0 0 59 45 820 0 924 43.8 Supplementary Table 1. Mapped DNA sequence reads for environmental- and subsistence-related taxa detected in this study. Statistically-significant ( i.e ., verified ancient) C-T p -values are indicated in bold text. Analyses were performed using high-quality filtered read alignments against NCBI reference genomes. DNA damage estimation analyses was performed using PMDtools (‘C-T p -values’). E-LPC BWA aligned (mapped) sequence reads Mean read C-T p -value Class Taxon Common name reads BRS1 BRS2 BRS3 BRS4 BRS5 Total length (bp) BRS1 BRS2 BRS3 BRS4 BRS5 Aconoidasida Babesia bovis Protozoan parasite 0 0 59 45 820 0 924 43.8 − 0.0273139 0.0314666 0.3810030 − Bacilli Lactococcus lactis Bacterium 0 100 541 340 4818 0 5799 70.6 0.5582629 0.0027567 0.0355133 0.0000015 − Dicotyledonae Ficus sur Cluster fig 0 6 179 59 1171 2 1417 67.0 0.3958356 0.0120650 0.5833718 0.0334960 0.5000000 Secernentea Parastrongyloides trichosuri Nematode parasite 0 11 1281 447 8481 13 10233 65.0 0.5337832 0.0253805 0.2410555 0.0528887 0.5085527 Sordariomycetes Podospora anserina Ascomycete fungus 0 1 16 6 466 2 491 61.4 − 0.1799564 0.5000000 0.3874920 − Sorghum bicolor Sorghum or durra 0 297 371 221 4359 166 5414 70.2 0.1020672 0.0066557 0.9053457 0.0000108 0.8410222 Monocotyledonae Triticum aestivum Common wheat 0 290 335 153 2826 505 4109 64.0 0.4611596 0.2830501 0.1544875 0.4358290 0.5196183 Zea mays Maize or corn 1 81 205 122 2661 0 3070 54.8 0.0718288 0.5123976 0.6440315 0.1234000 − Bos taurus Domestic cattle 0 847 459 281 26215 91 27893 62.8 0.7214745 0.3237143 0.2069171 0.1183520 0.0844617 Canis lupus familiaris Domestic dog 0 0 0 0 0 71 71 51.4 − − − − 0.7881283 Canis mesomelas Black-backed jackal 0 0 0 0 0 0 0 − − − − − − Capra hircus Domestic goat 0 1390 325 238 40118 117 42188 63.4 0.0580973 0.0132379 0.3843594 0.0000900 0.1955150 Caracal caracal Caracal or rooikat 0 0 0 0 0 0 0 − − − − − − Cercopithecus aethiops Vervet monkey 0 0 0 0 0 0 0 − − − − − − Equus caballus Modern horse 0 126 170 68 1395 79 1838 51.2 0.4765005 0.3077120 0.7492095 0.0007678 0.1313032 Mammalia Homo sapiens Human 56 335 270 117 1580 104 2462 61.2 0.6122221 0.0058446 0.7521352 0.0366582 0.1393800 Ictonyx striatus Striped polecat 0 0 0 0 0 0 0 − − − − − − Macaca mulatta Rhesus macaque 0 296 247 114 4593 96 5346 58.0 0.4855835 0.1070172 0.7493560 0.0269014 0.2207390 Mellivora capensis Honey badger 0 0 0 0 0 0 0 − − − − − − Ovis aries Domestic sheep 0 1026 289 206 36490 100 38111 62.6 0.0226299 0.1273375 0.2981717 0.0086748 0.1452299 Pan troglodytes Chimpanzee 0 390 276 111 2346 90 3213 60.6 0.5325693 0.0025637 0.7734403 0.0398303 0.3383619 Panthera pardus Leopard 0 0 0 0 0 0 0 − − − − − − Papio ursinus Chachma baboon 0 0 0 0 0 0 0 − − − − − − Total 57 5196 5023 2528 138339 1436 152579 60.5 − − − − Supplementary Table 2. Information concerning the two direct radiocarbon (14C) Accelerator Mass Spectrometry (AMS) dates generated from two sub-samples taken from within the BRS palaeo-faecal specimen. Sample Lab # 13C pMC pMC_err conv_age age_err BRS1 IT-C-1020 -16.79 94.37 0.524 470.2 44.1 BRS2 IT-C-1077 -16.79 94.39 0.416 460.2 35.0 Supplementary Table 3a. Processing protocol and results for isotope analyses of samples derived from the BRS specimen indicating the relative proportions of C3 and C4 dietary contributions. Sample Weight N peak 15N corr %N C peak 13C corr %C C/N BRS COP 1 0.82 12.66 11.28 1.52% 19.49 -17.93 22.46% 17.20 BRS COP 2 0.89 13.58 11.22 1.53% 20.84 -17.18 22.27% 16.95 BRS COP 3 0.84 13.36 11.45 1.58% 22.03 -17.65 24.78% 18.29 BRS LX 1 0.81 13.86 10.87 1.71% 21.89 -17.01 25.53% 17.44 BRS LX 2 0.84 14.16 10.98 1.69% 21.30 -16.98 23.95% 16.57 BRS LX 3 0.90 14.15 11.18 1.58% 21.69 -17.27 22.85% 16.92 BRS Acid 1 0.89 11.72 10.93 1.26% 23.78 -16.34 25.22% 23.39 BRS Acid 2 0.86 10.74 10.83 1.17% 24.36 -17.63 26.73% 26.69 BRS Acid 3 0.85 11.35 10.92 1.26% 23.14 -16.40 25.63% 23.74 BRS CS 1 1.04 22.14 11.10 2.23% 39.95 -23.08 36.27% 18.96 BRS CS 2 0.88 18.93 11.12 2.21% 33.38 -23.16 35.84% 18.88 BRS CS 3 1.03 21.77 11.05 2.21% 39.73 -23.60 36.52% 19.26 Supplementary Table 3b. Results for isotope analyses (Merck standard) of samples derived from the BRS specimen indicating the relative proportions of C3 and C4 dietary contributions. Weight N peak N C peak C Merck 0.22 29.65 7.82 9.43 -20.28 Merck 0.41 56.33 7.95 17.96 -20.23 Merck 0.60 82.27 7.97 26.34 -20.26 Merck 0.24 34.14 7.81 10.24 -20.27 Merck 0.40 57.99 7.92 17.83 -20.28 Merck 0.60 89.53 7.78 26.13 -20.22 Merck 0.23 36.75 7.91 10.33 -20.27 Merck 0.41 61.18 7.98 18.12 -20.28 Merck 0.64 92.49 7.95 28.44 -20.25 Merck 0.64 92.85 7.80 28.68 -20.26 7.89 -20.26 0.08 0.02 Supplementary Table 3c. Results for isotope analyses (DL-Valine standard) of samples derived from the BRS specimen indicating the relative proportions of C3 and C4 dietary contributions. Weight N peak N C peak C DL-Valine 0.23 24.84 -6.10 12.09 -10.56 DL-Valine 0.41 44.35 -6.22 21.92 -10.53 DL-Valine 0.63 66.39 -6.15 33.12 -10.68 DL-Valine 0.21 24.24 -6.13 11.07 -10.51 DL-Valine 0.44 50.16 -6.09 23.54 -10.54 DL-Valine 0.60 68.98 -6.21 32.72 -10.56 DL-Valine 0.23 29.22 -6.19 12.15 -10.61 DL-Valine 0.42 49.46 -6.12 22.52 -10.63 DL-Valine 0.62 70.56 -6.16 33.30 -10.55 DL-Valine 0.62 70.17 -6.13 32.95 -10.53 -6.15 -10.57 0.04 0.05 Supplementary Table 4. Assignment of abundance of bacterial taxonomic categories to the BRS and ancient (Ötzi) and modern (Italian, Hadza and Malawian) comparative samples based onp -value (p ꞊ <0.05) designation. Group significance assignments were obtained via Qiime v1.9.1. OTU Test-Statistic P BRS_mean Otzi-UPLI_mean Otzi-SI_mean Otzi-LPLI_mean Hadza_mean Malawi_mean Italian_mean Taxonomy ID251698 17.978824 0.006285 1.00 20.50 26.00 5.00 0.00 0.00 0.00 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas; s__(Pseudomonas) ID47877 17.978824 0.006285 3.00 70.50 94.00 12.00 0.00 0.00 0.00 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas; s__Pseudomonas amygdali ID40215 17.978673 0.006286 2.00 17.00 5.00 2.00 0.00 0.00 0.00 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Moraxellaceae; g__Acinetobacter; s__Acinetobacter junii ID162481 17.968966 0.006310 0.00 260.00 191.00 9.00 0.00 0.00 0.00 k__Eukaryota; p__Basidiomycota; c__Microbotryomycetes; o__(Microbotryomycetes); f__(Microbotryomycetes); g__(Microbotryomycetes); s__(Microbotryomycetes) ID288795 17.968966 0.006310 0.00 501.00 248.00 8.00 0.00 0.00 0.00 k__Eukaryota; p__Basidiomycota; c__Microbotryomycetes; o__Microbotryales; f__Microbotryaceae; g__Microbotryum; s__Microbotryum lychnidis-dioicae ID5286 17.968966 0.006310 0.00 218.50 148.00 6.00 0.00 0.00 0.00 k__Eukaryota; p__Basidiomycota; c__Microbotryomycetes; o__Sporidiobolales; f__Sporidiobolaceae; g__Rhodotorula; s__Rhodotorula toruloides ID65741 17.936620 0.006393 3.33 6.00 8.00 1.00 0.00 0.00 0.00 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas; s__Pseudomonas knackmussii ID351095 17.929961 0.006410 70.67 1.00 0.00 1.00 0.00 0.00 0.00 k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Bacillaceae; g__Paucisalibacillus; s__Paucisalibacillus globulus ID109871 17.929961 0.006410 7.33 1.00 0.00 1.00 0.00 0.00 0.00 k__Eukaryota; p__Chytridiomycota; c__Chytridiomycetes; o__Rhizophydiales; f__(Batrachochytrium); g__Batrachochytrium; s__Batrachochytrium dendrobatidis ID40214 17.915592 0.006447 4.67 346.50 1.00 106.00 0.00 0.00 0.00 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Moraxellaceae; g__Acinetobacter; s__Acinetobacter johnsonii ID1439940 17.915592 0.006447 13.00 3.00 5.00 1.00 0.00 0.00 0.00 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas; s__Pseudomonas sp. BAY1663 ID157784 17.915592 0.006447 15.00 4.00 5.00 1.00 0.00 0.00 0.00 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas; s__Pseudomonas thermotolerans ID706570 17.914692 0.006449 591.33 1.00 1.00 1.00 0.00 0.00 0.00 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas; s__Pseudomonas flexibilis ID5061 17.914692 0.006449 8.00 1.00 1.00 1.00 0.00 0.00 0.00 k__Eukaryota; p__Ascomycota; c__Eurotiomycetes; o__Eurotiales; f__Aspergillaceae; g__Aspergillus; s__Aspergillus niger ID5073 17.914692 0.006449 19.00 1.00 1.00 1.00 0.00 0.00 0.00 k__Eukaryota; p__Ascomycota; c__Eurotiomycetes; o__Eurotiales; f__Aspergillaceae; g__Penicillium; s__(Penicillium) ID37914 17.906736 0.006470 26.00 1.00 0.00 1.00 0.00 0.00 0.00 k__Bacteria; p__Actinobacteria <phylum>; c__Actinobacteria; o__Corynebacteriales; f__Dietziaceae; g__Dietzia; s__(Dietzia) ID558169 17.906736 0.006470 67.67 1.00 0.00 1.00 0.00 0.00 0.00 k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Bacillaceae; g__Lentibacillus; s__Lentibacillus jeotgali ID694055 17.906736 0.006470 19.00 1.00 0.00 1.00 0.00 0.00 0.00 k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Bacillaceae; g__Ornithinibacillus; s__Ornithinibacillus contaminans ID403957 17.906736 0.006470 17.33 1.00 0.00 1.00 0.00 0.00 0.00 k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Bacillaceae; g__Virgibacillus; s__Virgibacillus sp.
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