Supplementary data: Comparison of target enrichment strategies for ancient pathogen DNA

<b>Supplementary Note 1 – Laboratory
workflow</b>
<b> </b>
<b>Supplementary Note 2 -
Bioinformatics and Statistical Analysis</b>
<b> </b>
<b>Supplementary Note 3 – Results of
the Bioinformatics and Statistical Analysis</b>
<b> </b>
<b>Supplementary Figure 1: Comparison
of (A) mean coverage, (B) standard deviation of the mean coverage, (C)
enrichment factor, (D) and the percentage of the genome covered 5 fold, (E)
distribution of the fragment length and (F) frequency of the aDNA damage for
the ancient and modern strains of <i>M. leprae</i>.</b> Three independent replicates were
performed for each method. Labels of the ancient samples are in black and for
the modern samples in red. Boxplots of the array are blue, of the DNA bait
capture red and the RNA baits capture is green and grey for the first and
second round, respectively

<b>Supplementary Figure 2: Comparison of (A) mean
coverage, (B) standard deviation of the mean coverage, (C) enrichment factor,
(D) and the percentage of the genome covered 5 fold, (E) distribution of the
fragment length and (F) frequency of the aDNA damage for the ancient and modern
strains of <i>T. pallidum</i>.</b>
Three independent replicates were performed for each method. Labels of the
ancient samples are in black and for the modern samples in red. Boxplots of the
array are

blue, of the DNA bait capture red
and the RNA baits capture is green and grey for the first and second round,
respectively

<b>Supplementary Figure
3: Number of unique reads for the three replicate batches of the three tested
methods. </b>The number of unique reads in the second round of hybridization
with the RNA baits does not strongly increase compared to the first round.

Supplementary Table 1:
List of all samples used in this study group according to organism and age
together with the original publications.
Supplementary Table
4: Comparison of the specific reads of the three tested protocols.
Supplementary Table
6: Comparison of the variance within each method tested.

Supplementary Table 7: Comparison of the costs
per reaction.