Verification of assay on amplified libraries with shotgun sequencing data.

1<p>As discussed in the methods section, the assay percentages are meant as a guide to compare samples and are not expected to match the absolute values yielded via shotgun sequencing.</p>2<p>The scaled shotgun sequencing results do not include reads without BLAST matches or reads which matched higher taxonomic levels (e.g., eukaryotes or metazoa).</p>3<p><i>N/A</i> indicates the primer set did not fluoresce before the negative control for the sample.</p

Archaeobotanical samples tested in assay.

<p>Archaeobotanical samples tested in assay.</p

Directions to interpret qPCR assay data.

<p>Follow the questions in the flowchart to compare the endogenous DNA content of different ancient plant samples. The least contaminated samples are best suited for shotgun sequencing.</p

Primers for qPCR contamination assay.

<p>Primers for qPCR contamination assay.</p

Archaeobotanical remains analyzed.

<p>Archaeobotanical remains analyzed.</p

Extraction techniques compared in this study.

<p>Extraction techniques compared in this study.</p

Amplification of spiked DNA in the presence of inhibiting substances.

<p>Amplification of spiked DNA in the presence of inhibiting substances.</p

Polymerases tested.

<p>Polymerases tested.</p

DNA yield from extractions, phase 2.

<p>Maximum amount of DNA recovered in each specimen listed by corresponding symbol.</p

Error rates of most frequent substitution types.

<p>High-low chart depicts the maximum and minimum error rates within the three tested samples. Median values, represented by circles, are not included for PfuTurbo C_x because only two samples were amplified.</p